Pan-UKB Pleitropy of Diseases v01

Author

Saikat Banerjee

Published

December 11, 2023

Abstract

We look at the pleiotropy of some common diseases from the Pan-UKB data.

Getting Setup

Code

import numpy as np
import pandas as pd
import pickle

import matplotlib.pyplot as plt
from pymir import mpl_stylesheet
from pymir import mpl_utils
mpl_stylesheet.banskt_presentation(splinecolor = 'black', dpi = 120, colors = 'kelly')
from matplotlib.gridspec import GridSpec

from nnwmf.optimize import IALM
from nnwmf.optimize import FrankWolfe, FrankWolfe_CV
from nnwmf.utils import model_errors as merr

import sys
sys.path.append("../utils/")
import simulate as mpy_simulate

Load data and results

Code

data_dir = "/gpfs/commons/home/sbanerjee/work/npd/PanUKB/data"
result_dir = "/gpfs/commons/home/sbanerjee/work/npd/PanUKB/nnwmf"
zscore_filename = f"{data_dir}/GWAS_Zscore.tsv"
trait_filename = f"{data_dir}/trait_manifest_TableS6_no_readme.tsv"
zscore_df = pd.read_csv(zscore_filename, sep = '\t')
trait_df = pd.read_csv(trait_filename, sep = '\t')

# remove extra columns from trait_df

colnames = trait_df.columns.tolist()
colnames[0] = "zindex"
trait_df.columns = colnames
trait_df_mod = trait_df.drop(labels = ['coding', 'modifier', 'coding_description', 'filename', 'aws_link'], axis=1)
trait_df_mod['trait_name'] = trait_df_mod['description']
trait_df_mod['trait_name'] = trait_df_mod['trait_name'].fillna(trait_df_mod['phenocode'])

Code

X_nan = np.array(zscore_df.loc[:, zscore_df.columns!='rsid']).T
X_nan_cent = X_nan - np.nanmean(X_nan, axis = 0, keepdims = True)
X_nan_mask = np.isnan(X_nan)
X_cent = np.nan_to_num(X_nan_cent, copy = True, nan = 0.0)

print (f"We have {X_cent.shape[0]} samples (phenotypes) and {X_cent.shape[1]} features (variants)")
print (f"Fraction of Nan entries: {np.sum(X_nan_mask) / np.prod(X_cent.shape):.3f}")

We have 2483 samples (phenotypes) and 51399 features (variants)
Fraction of Nan entries: 0.000

Code

mf_methods = ['ialm', 'nnm_sparse', 'tsvd']

method_prefix = {
    'ialm' : 'ialm_maxiter10000_admm',
    'nnm_sparse' : 'nnm_sparse_maxiter1000'
}

method_names = {
    'tsvd' : 'Raw Data',
    'ialm' : 'RPCA-IALM',
    'nnm'  : 'NNM-FW',
    'nnm_weighted' : 'NNM-Weighted',
    'nnm_sparse' : 'NNM-Sparse-FW',
}

with open (f"{result_dir}/{method_prefix['ialm']}_progress.pkl", 'rb') as handle:
    ialm = pickle.load(handle)
    
with open (f"{result_dir}/{method_prefix['nnm_sparse']}_progress.pkl", 'rb') as handle:
    nnm_sparse = pickle.load(handle)

Code

def get_principal_components(X):
    X_cent = mpy_simulate.do_standardize(X, scale = False)
    X_cent /= np.sqrt(np.prod(X_cent.shape))
    U, S, Vt = np.linalg.svd(X_cent, full_matrices = False)
    pcomps = U @ np.diag(S)
    loadings = Vt.T @ np.diag(S)
    return loadings, pcomps, S

lowrank_X = dict()
loadings  = dict()
pcomps    = dict()
eigenvals = dict()

for m in mf_methods:
    if m != 'tsvd':
        with open (f"{result_dir}/{method_prefix[m]}_lowrank_X.pkl", 'rb') as handle:
            lowrank_X[m] = pickle.load(handle)
lowrank_X['tsvd'] = X_cent.copy()
for m in mf_methods:
    loadings[m], pcomps[m], eigenvals[m] = get_principal_components(lowrank_X[m])

Code

def get_cos2_scores(pcomps):
    ntrait, npcomp = pcomps.shape
    x = np.zeros((ntrait, npcomp))
    std_pcomps = pcomps / np.sqrt(np.var(pcomps[:,:], axis = 0))
    for i in range(ntrait):
        cos2_trait = np.array([np.square(std_pcomps[i, pcidx]) for pcidx in range(npcomp)])
        x[i, :] = cos2_trait / np.sum(cos2_trait)
    return x

def get_contribution_scores(pcomps):
    ntrait, npcomp = pcomps.shape
    x = np.zeros((ntrait, npcomp))
    std_pcomps = pcomps / np.sqrt(np.var(pcomps[:,:], axis = 0)).reshape(1, -1)
    for i in range(npcomp):
        trait_contr = np.array([np.square(std_pcomps[j, i]) for j in range(ntrait)])
        x[:, i] = trait_contr / np.sum(trait_contr)
    return x

npcomp = 100
cos2_scores = dict()
for m in mf_methods:
    cos2_scores[m] = get_cos2_scores(pcomps[m][:,:npcomp])

trait_contributions = dict()
for m in mf_methods:
    trait_contributions[m] = get_contribution_scores(pcomps[m][:,:npcomp])

Pleiotropy

In the following, we look at the pleiotropy of different diseases reported in the UKB project. Given a phenotype (focal trait), we find the hidden factor with the highest contribution to the focal trait. We then report the other phenotypes which contribute to that hidden factor.

Function pan_ukb_pleiotropy(trait_index)

Input: - Index of the focal trait as found in the manifest file. - Number of pleiotropic traits to be reported (optional, default 15).

Output: - Index of the top hidden factor. - Contribution of the hidden factor on the focal trait. - List of pleiotropic traits, and their contributions to the hidden factor.

Global Variables: trait_df_mod, mf_methods, cos2_scores, trait_contributions, method_names

Code

from IPython.display import Markdown, display
from IPython.core.display import HTML

import re
def titlecase(s):
    return re.sub(r"[A-Za-z]+('[A-Za-z]+)?", lambda mo: mo.group(0).capitalize(),s)

def print_markdown(string, color = None):
    colorstr = "<span style='color:{}'>{}</span>".format(color, string)
    display(Markdown(colorstr))
    
def print_header(string):
    headerstr=f"<h2>{string}</h2>"
    display(Markdown(headerstr))
    
def print_table(list1, list2):
    #table_css = 'table {align:left;display:block}'
    tablestr = "<table style={float:left; align:left;}>"
    for l1, l2 in zip(list1, list2):
        tablestr += f"<tr><td>{l1:.4f}</td><td>{l2}</td></tr>"
    tablestr +="</table>"
    display(Markdown(tablestr))
            
def pan_ukb_pleiotropy(znum, num_trait = 15):
    zindex = znum - 1
    focal_trait_name = trait_df_mod.loc[zindex, 'trait_name']
    print_header(titlecase(focal_trait_name))
    for m in mf_methods:
        print_markdown (f"**{method_names[m]}**", color = "#c8635a")
        top_factor = np.argsort(cos2_scores[m][zindex,:])[::-1][0]
        print_markdown (f"Top Factor: {top_factor + 1} (Contribution: {cos2_scores[m][zindex,top_factor]:.4f})")
        top_traits = np.argsort(trait_contributions[m][:,top_factor])[::-1][:num_trait]
        trait_names = trait_df_mod.loc[top_traits]['trait_name'].tolist()
        print_table(trait_contributions[m][top_traits, top_factor], trait_names)

def pan_ukb_pleiotropy_(znum, num_trait = 15):
    zindex = znum - 1
    focal_trait_name = trait_df_mod.loc[zindex, 'trait_name']
    printheader(titlecase(focal_trait_name))
    for m in mf_methods:
        printmd (f"**{method_names[m]}**", color = "#c8635a")
        top_factor = np.argsort(cos2_scores[m][zindex,:])[::-1][0]
        printmd(f"Top Factor: {top_factor + 1} (Contribution: {cos2_scores[m][zindex,top_factor]:.4f})")
        top_traits = np.argsort(trait_contributions[m][:,top_factor])[::-1][:num_trait]
        trait_names = trait_df_mod.loc[top_traits]['trait_name'].tolist()
        for i, x in zip(top_traits, trait_names):
            print(f"    {trait_contributions[m][i, top_factor]:.4f}   {x}")
        print(f"")

Common Diseases

Code

pan_ukb_pleiotropy(930)

Rheumatoid Arthritis

RPCA-IALM

Top Factor: 47 (Contribution: 0.1697)

0.0236	methotrexate
0.0236	anti-metabolite
0.0167	folic acid supplement\|Food Supplement
0.0167	folic acid
0.0146	Forced expiratory volume in 1-second (FEV1), Best measure
0.0141	Forced expiratory volume in 1-second (FEV1)
0.0131	Forced vital capacity (FVC), Best measure
0.0126	Forced vital capacity (FVC)
0.0113	anti-inflammatory
0.0113	sulfasalazine
0.0104	Rheumatoid arthritis
0.0097	Neutrophill percentage
0.0097	Rheumatoid arthritis and other inflammatory polyarthropathies
0.0095	Corneal resistance factor (left)
0.0093	Corneal resistance factor (right)

NNM-Sparse-FW

Top Factor: 88 (Contribution: 0.0664)

0.0319	Whole body fat-free mass
0.0251	Leg fat percentage (right)
0.0194	Hand grip strength (left)
0.0120	Leg predicted mass (right)
0.0118	Forced vital capacity (FVC), Best measure
0.0110	codine/paracetamol
0.0103	Arm fat-free mass (right)
0.0099	Mean arterial pressure, automated reading
0.0096	Trunk fat-free mass
0.0096	Peak expiratory flow (PEF)
0.0092	Trunk predicted mass
0.0090	Basal metabolic rate
0.0089	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0071	Arm fat mass (left)
0.0069	Age completed full time education

Raw Data

Top Factor: 73 (Contribution: 0.1319)

0.0213	I35 Nonrheumatic aortic valve disorders
0.0211	Nonrheumatic aortic valve disorders
0.0173	Congenital anomalies of great vessels
0.0157	Cardiac congenital anomalies
0.0147	Cardiac and circulatory congenital anomalies
0.0137	Albumin
0.0128	anti-metabolite
0.0128	methotrexate
0.0126	Heart valve disorders
0.0094	Aortic valve disease
0.0093	Rheumatoid arthritis
0.0090	Rheumatoid arthritis and other inflammatory polyarthropathies
0.0080	Osteoporosis
0.0080	Osteoporosis NOS
0.0080	Treatment/medication code

Code

pan_ukb_pleiotropy(420)

Cancer Of Prostate

RPCA-IALM

Top Factor: 78 (Contribution: 0.0875)

0.0272	Contracture of palmar fascia [Dupuytren's disease]
0.0262	Disorders of muscle, ligament, and fascia
0.0243	Fasciitis
0.0186	Malignant neoplasm of bladder
0.0182	C67 Malignant neoplasm of bladder
0.0157	Cancer of bladder
0.0156	M72 Fibroblastic disorders
0.0131	K76 Other diseases of liver
0.0130	Other disorders of liver
0.0127	Sebaceous cyst
0.0125	Diseases of sebaceous glands
0.0114	Prostatitis
0.0112	Chronic liver disease and cirrhosis
0.0110	L72 Follicular cysts of skin and subcutaneous tissue
0.0107	Cancer of urinary organs (incl. kidney and bladder)

NNM-Sparse-FW

Top Factor: 48 (Contribution: 0.0815)

0.0247	Weight
0.0190	Whole body water mass
0.0134	Trunk fat mass
0.0132	Age at first live birth
0.0128	Weight
0.0123	Arm fat-free mass (left)
0.0119	Overweight, obesity and other hyperalimentation
0.0112	Body mass index (BMI)
0.0108	Leg fat percentage (right)
0.0089	Hip circumference
0.0088	Leg fat-free mass (right)
0.0081	Trunk predicted mass
0.0064	aspirin
0.0064	Leg fat-free mass (left)
0.0063	sodium alginate / potassium bicarbonate

Raw Data

Top Factor: 54 (Contribution: 0.0663)

0.0277	Albumin
0.0221	IGF-1
0.0168	Calcium
0.0163	Alkaline phosphatase
0.0114	Corneal resistance factor (left)
0.0106	Corneal resistance factor (right)
0.0098	Total protein
0.0089	Corneal hysteresis (left)
0.0079	Corneal hysteresis (right)
0.0065	Phosphate
0.0065	Home location - east co-ordinate (rounded)
0.0063	Urate
0.0062	Home location at assessment - east co-ordinate (rounded)
0.0060	Other disorders of bladder
0.0056	Albumin/Globulin ratio

Code

pan_ukb_pleiotropy(410)

Breast Cancer

RPCA-IALM

Top Factor: 25 (Contribution: 0.1298)

0.0221	Breast cancer [female]
0.0215	Breast cancer
0.0210	Malignant neoplasm of female breast
0.0200	C50 Malignant neoplasm of breast
0.0167	Arthropathy NOS
0.0167	Other arthropathies
0.0129	M17 Gonarthrosis [arthrosis of knee]
0.0110	Osteoarthrosis
0.0108	Unspecified monoarthritis
0.0098	Diseases of esophagus
0.0095	Diaphragmatic hernia
0.0093	Osteoarthritis; localized
0.0091	K44 Diaphragmatic hernia
0.0090	Esophagitis, GERD and related diseases
0.0088	Malignant neoplasm, other

NNM-Sparse-FW

Top Factor: 66 (Contribution: 0.0840)

0.0300	Leg fat-free mass (right)
0.0273	Whole body fat-free mass
0.0264	Sitting height
0.0208	Arm fat-free mass (left)
0.0128	Impedance of leg (left)
0.0128	Body mass index (BMI)
0.0120	Arm predicted mass (right)
0.0109	Whole body water mass
0.0098	Type 2 diabetes
0.0097	Waist circumference
0.0097	Arm predicted mass (left)
0.0085	Arm fat-free mass (right)
0.0081	E66 Obesity
0.0078	Impedance of leg (right)
0.0074	lansoprazole

Raw Data

Top Factor: 48 (Contribution: 0.0812)

0.0133	Urate
0.0109	Past tobacco smoking
0.0108	Breast cancer
0.0108	Breast cancer [female]
0.0101	Malignant neoplasm of female breast
0.0099	C50 Malignant neoplasm of breast
0.0099	Smoking status, ever vs never
0.0090	Age first had sexual intercourse
0.0086	Alkaline phosphatase
0.0075	Diseases of esophagus
0.0072	Gamma glutamyltransferase
0.0071	Aspartate aminotransferase
0.0070	Esophagitis, GERD and related diseases
0.0067	Duration to first press of snap-button in each round
0.0062	Estimated glomerular filtration rate, serum creatinine + cystain C

Code

pan_ukb_pleiotropy(458)

Diabetes Mellitus

RPCA-IALM

Top Factor: 19 (Contribution: 0.1403)

0.0364	Red blood cell (erythrocyte) count
0.0189	Glycated haemoglobin (HbA1c)
0.0178	Mean corpuscular volume
0.0159	Lymphocyte count
0.0150	Mean sphered cell volume
0.0146	Haemoglobin concentration
0.0137	Platelet count
0.0136	Haematocrit percentage
0.0132	Mean corpuscular haemoglobin
0.0128	Type 2 diabetes
0.0127	Non-albumin protein
0.0124	E11 Non-insulin-dependent diabetes mellitus
0.0119	Diabetes mellitus
0.0108	Platelet crit
0.0106	Neutrophill percentage

NNM-Sparse-FW

Top Factor: 57 (Contribution: 0.0559)

0.0178	Arm fat-free mass (left)
0.0162	Trunk fat mass
0.0144	Body mass index (BMI)
0.0140	codine/paracetamol
0.0135	Type 2 diabetes
0.0131	Comparative height size at age 10
0.0107	tetracycline antibiotic\|antibiotic
0.0095	Impedance of arm (right)
0.0092	Hip circumference
0.0092	Diabetes mellitus
0.0089	Forced expiratory volume in 1-second (FEV1), Best measure
0.0082	ACE inhibitor\|anti-hypertensive
0.0077	Trunk fat-free mass
0.0069	trimethoprim
0.0069	Weight

Raw Data

Top Factor: 26 (Contribution: 0.1503)

0.1042	HDL cholesterol
0.0898	Apolipoprotein A
0.0473	Glycated haemoglobin (HbA1c)
0.0273	Albumin/Globulin ratio
0.0231	Non-albumin protein
0.0208	Platelet crit
0.0192	Neutrophill percentage
0.0175	Neutrophill count
0.0154	Lymphocyte percentage
0.0138	IGF-1
0.0131	Gamma glutamyltransferase
0.0112	Type 2 diabetes
0.0111	Diabetes mellitus
0.0111	E11 Non-insulin-dependent diabetes mellitus
0.0109	Mean platelet (thrombocyte) volume

Code

pan_ukb_pleiotropy(529)

Parkinson’s Disease

RPCA-IALM

Top Factor: 97 (Contribution: 0.0888)

0.0441	Psoriasis
0.0425	L40 Psoriasis
0.0403	Psoriasis and related disorders
0.0187	Cardiac arrest
0.0184	Cardiac arrest and ventricular fibrillation
0.0181	I46 Cardiac arrest
0.0117	K90 Intestinal malabsorption
0.0114	Intestinal malabsorption (non-celiac)
0.0109	Obesity
0.0108	E66 Obesity
0.0097	Overweight, obesity and other hyperalimentation
0.0095	Aortic aneurysm
0.0094	I71 Aortic aneurysm and dissection
0.0090	Celiac disease
0.0085	Noninflammatory disorders of ovary, fallopian tube, and broad ligament

NNM-Sparse-FW

Top Factor: 70 (Contribution: 0.0852)

0.0262	Trunk fat percentage
0.0240	Whole body fat-free mass
0.0207	Leg predicted mass (left)
0.0201	Arm fat-free mass (left)
0.0172	Leg fat percentage (left)
0.0147	Leg fat mass (right)
0.0105	Leg fat mass (left)
0.0083	NSAID\|non-steroidal anti-inflammatory drug
0.0079	Usual walking pace
0.0078	proton pump inhibitor\|PPI
0.0073	Impedance of leg (left)
0.0071	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0065	Arm fat mass (right)
0.0061	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0059	codine/paracetamol

Raw Data

Top Factor: 92 (Contribution: 0.1208)

0.0149	Urinary calculus
0.0149	N20 Calculus of kidney and ureter
0.0147	Maximum heart rate during fitness test
0.0146	ECG, load
0.0146	Maximum workload during fitness test
0.0139	Pulse rate, automated reading
0.0138	ECG, heart rate
0.0130	ECG, number of stages in a phase
0.0126	Number of trend entries
0.0117	ECG, phase time
0.0110	Calculus of ureter
0.0102	Processed meat intake
0.0101	Calculus of kidney
0.0088	Beef intake
0.0080	Lamb/mutton intake

Code

pan_ukb_pleiotropy(504)

Dementias

RPCA-IALM

Top Factor: 99 (Contribution: 0.1643)

0.0148	Cardiac arrest
0.0146	Cardiac arrest and ventricular fibrillation
0.0144	I46 Cardiac arrest
0.0130	Other disorders of pancreatic internal secretion
0.0125	Hypoglycemia
0.0122	E16 Other disorders of pancreatic internal secretion
0.0112	Obesity
0.0111	E66 Obesity
0.0104	E21 Hyperparathyroidism and other disorders of parathyroid gland
0.0104	G47 Sleep disorders
0.0103	Hyperparathyroidism
0.0101	Sleep disorders
0.0101	Overweight, obesity and other hyperalimentation
0.0090	Varicose veins of lower extremity
0.0088	Disorders of parathyroid gland

NNM-Sparse-FW

Top Factor: 74 (Contribution: 0.0601)

0.0203	Number of self-reported non-cancer illnesses
0.0169	Leg predicted mass (left)
0.0162	Waist circumference
0.0160	Hip circumference
0.0139	Mean arterial pressure, combined automated + manual reading
0.0136	Arm fat mass (left)
0.0130	Diastolic blood pressure, combined automated + manual reading
0.0129	NSAID\|non-steroidal anti-inflammatory drug
0.0129	Arm fat-free mass (left)
0.0128	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0128	Impedance of arm (left)
0.0109	Essential hypertension
0.0106	Body mass index (BMI)
0.0098	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0092	Peak expiratory flow (PEF)

Raw Data

Top Factor: 61 (Contribution: 0.0862)

0.0324	Heel bone mineral density (BMD)
0.0322	Heel bone mineral density (BMD) T-score, automated
0.0322	Heel quantitative ultrasound index (QUI), direct entry
0.0258	Heel Broadband ultrasound attenuation, direct entry
0.0139	Urate
0.0119	Heel bone mineral density (BMD) T-score, automated (left)
0.0119	Heel quantitative ultrasound index (QUI), direct entry (left)
0.0119	Heel broadband ultrasound attenuation (left)
0.0116	Heel bone mineral density (BMD) (left)
0.0115	Heel bone mineral density (BMD) T-score, automated (right)
0.0115	Heel quantitative ultrasound index (QUI), direct entry (right)
0.0115	Heel broadband ultrasound attenuation (right)
0.0114	Heel bone mineral density (BMD) (right)
0.0103	Cerebrovascular disease
0.0102	Creatinine

Code

pan_ukb_pleiotropy(61)

G47 Sleep Disorders

RPCA-IALM

Top Factor: 86 (Contribution: 0.1228)

0.0469	Acquired foot deformities
0.0468	M20 Acquired deformities of fingers and toes
0.0290	Hemoptysis
0.0286	R04 Haemorrhage from respiratory passages
0.0275	Obesity
0.0272	E66 Obesity
0.0272	Hallux valgus (Bunion)
0.0253	Acquired toe deformities
0.0248	Abnormal sputum
0.0247	Overweight, obesity and other hyperalimentation
0.0123	G47 Sleep disorders
0.0119	Sleep disorders
0.0111	Hammer toe (acquired)
0.0110	Epistaxis or throat hemorrhage
0.0095	Prostatitis

NNM-Sparse-FW

Top Factor: 43 (Contribution: 0.0683)

0.0234	ACE inhibitor\|anti-hypertensive
0.0141	High light scatter reticulocyte count
0.0133	Usual walking pace
0.0121	Weight
0.0119	Leg predicted mass (left)
0.0109	Trunk fat-free mass
0.0104	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0100	Reticulocyte count
0.0092	Trunk fat percentage
0.0091	Waist circumference
0.0081	Age first had sexual intercourse
0.0077	Seated height
0.0066	Treatment/medication code
0.0064	Other arthropathies
0.0061	Ankle spacing width (right)

Raw Data

Top Factor: 91 (Contribution: 0.1037)

0.0136	Aspartate aminotransferase
0.0125	Platelet distribution width
0.0112	Alanine aminotransferase
0.0084	Inflammatory bowel disease and other gastroenteritis and colitis
0.0074	Spherical power (right)
0.0070	Genital prolapse
0.0070	Prolapse of vaginal walls
0.0069	Spherical power (left)
0.0068	N81 Female genital prolapse
0.0068	Open wounds of head; neck; and trunk
0.0063	C79 Secondary malignant neoplasm of other sites
0.0061	E87 Other disorders of fluid, electrolyte and acid-base balance
0.0061	Ulcerative colitis
0.0061	Electrolyte imbalance
0.0061	I77 Other disorders of arteries and arterioles

Code

pan_ukb_pleiotropy(59)

G43 Migraine

RPCA-IALM

Top Factor: 80 (Contribution: 0.0792)

0.0312	Appendicitis
0.0307	Acute appendicitis
0.0287	Appendiceal conditions
0.0284	K35 Acute appendicitis
0.0208	Sebaceous cyst
0.0203	Diseases of sebaceous glands
0.0186	L72 Follicular cysts of skin and subcutaneous tissue
0.0140	Contracture of palmar fascia [Dupuytren's disease]
0.0134	Disorders of muscle, ligament, and fascia
0.0133	Iron deficiency anemias, unspecified or not due to blood loss
0.0133	Iron deficiency anemias
0.0121	Fasciitis
0.0118	D50 Iron deficiency anaemia
0.0115	Home location - north co-ordinate (rounded)
0.0113	Home location at assessment - north co-ordinate (rounded)

NNM-Sparse-FW

Top Factor: 46 (Contribution: 0.0576)

0.0320	Leg predicted mass (right)
0.0257	Whole body fat-free mass
0.0243	Leg fat-free mass (right)
0.0192	Body mass index (BMI)
0.0167	Leg fat mass (left)
0.0144	NSAID\|non-steroidal anti-inflammatory drug
0.0120	simvastatin
0.0112	thiazide diuretic\|diuretic
0.0109	aspirin
0.0092	lansoprazole
0.0091	ACE inhibitor\|anti-hypertensive
0.0089	Diastolic blood pressure, automated reading
0.0085	Non-cancer illness code, self-reported
0.0070	bendroflumethiazide
0.0070	amoxicillin

Raw Data

Top Factor: 56 (Contribution: 0.0733)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

Code

pan_ukb_pleiotropy(591)

Hypertension

RPCA-IALM

Top Factor: 2 (Contribution: 0.0982)

0.0595	Standing height
0.0290	Sitting height
0.0227	Seated height
0.0197	Forced vital capacity (FVC)
0.0193	Forced vital capacity (FVC), Best measure
0.0169	Mean arterial pressure, combined automated + manual reading, adjusted by medication
0.0163	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0157	Comparative height size at age 10
0.0157	Forced expiratory volume in 1-second (FEV1)
0.0156	Mean arterial pressure, automated reading, adjusted by medication
0.0152	Forced expiratory volume in 1-second (FEV1), predicted
0.0150	Forced expiratory volume in 1-second (FEV1), Best measure
0.0149	Systolic blood pressure, automated reading, adjusted by medication
0.0138	Trunk fat-free mass
0.0138	Trunk predicted mass

NNM-Sparse-FW

Top Factor: 15 (Contribution: 0.1904)

0.0670	Essential hypertension
0.0596	Hypertension
0.0278	E78 Disorders of lipoprotein metabolism and other lipidaemias
0.0271	Disorders of lipoid metabolism
0.0265	Hypercholesterolemia
0.0256	Hyperlipidemia
0.0252	Ischemic Heart Disease
0.0197	Other chronic ischemic heart disease, unspecified
0.0174	I25 Chronic ischaemic heart disease
0.0138	antipyretic
0.0138	paracetamol
0.0134	opioid analgesic\|antipyretic
0.0130	Angina pectoris
0.0111	E11 Non-insulin-dependent diabetes mellitus
0.0100	Leg fat mass (left)

Raw Data

Top Factor: 3 (Contribution: 0.1210)

0.0461	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0425	Systolic blood pressure, automated reading, adjusted by medication
0.0405	Mean arterial pressure, combined automated + manual reading, adjusted by medication
0.0373	Mean arterial pressure, automated reading, adjusted by medication
0.0353	Systolic blood pressure, combined automated + manual reading
0.0334	Systolic blood pressure, automated reading
0.0304	Pulse pressure, combined automated + manual reading, adjusted by medication
0.0288	Mean arterial pressure, combined automated + manual reading
0.0282	Pulse pressure, automated reading, adjusted by medication
0.0277	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0274	Mean arterial pressure, automated reading
0.0261	Diastolic blood pressure, automated reading, adjusted by medication
0.0246	Pulse pressure, combined automated + manual reading
0.0235	Pulse pressure, automated reading
0.0180	Diastolic blood pressure, combined automated + manual reading

Code

pan_ukb_pleiotropy(2350)

Standing Height

RPCA-IALM

Top Factor: 7 (Contribution: 0.2952)

0.0748	Impedance of whole body
0.0676	Standing height
0.0580	Impedance of arm (left)
0.0572	Impedance of arm (right)
0.0569	Impedance of leg (left)
0.0559	Impedance of leg (right)
0.0233	Sitting height
0.0217	Seated height
0.0181	Comparative height size at age 10
0.0144	Forced expiratory volume in 1-second (FEV1), predicted
0.0132	Trunk fat percentage
0.0101	Body mass index (BMI)
0.0098	Body mass index (BMI)
0.0095	Reticulocyte count
0.0094	Heel quantitative ultrasound index (QUI), direct entry (right)

NNM-Sparse-FW

Top Factor: 4 (Contribution: 0.1740)

0.1274	Standing height
0.0721	Sitting height
0.0263	Seated height
0.0192	Comparative height size at age 10
0.0190	Trunk fat-free mass
0.0189	Trunk predicted mass
0.0134	Whole body fat-free mass
0.0117	Whole body water mass
0.0114	Waist circumference
0.0112	Leg fat mass (left)
0.0112	Arm fat mass (right)
0.0107	Leg fat mass (right)
0.0101	Arm fat mass (left)
0.0099	E66 Obesity
0.0099	Obesity

Raw Data

Top Factor: 2 (Contribution: 0.2623)

0.0640	Standing height
0.0351	Sitting height
0.0250	Seated height
0.0206	Forced vital capacity (FVC)
0.0197	Forced vital capacity (FVC), Best measure
0.0186	Comparative height size at age 10
0.0170	Forced expiratory volume in 1-second (FEV1), predicted
0.0161	Forced expiratory volume in 1-second (FEV1)
0.0152	Forced expiratory volume in 1-second (FEV1), Best measure
0.0132	Mean arterial pressure, combined automated + manual reading, adjusted by medication
0.0126	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0121	Mean arterial pressure, automated reading, adjusted by medication
0.0120	Leg fat percentage (left)
0.0120	Leg fat percentage (right)
0.0118	Trunk fat-free mass

Code

pan_ukb_pleiotropy(1747)

Intake Of Sugar Added To Coffee

RPCA-IALM

Top Factor: 52 (Contribution: 0.1127)

0.0152	Saturated fat
0.0138	Albumin
0.0124	Fat
0.0108	Osteoporosis
0.0108	Osteoporosis NOS
0.0093	Vitamin C
0.0086	Home location - north co-ordinate (rounded)
0.0084	methotrexate
0.0084	anti-metabolite
0.0081	Retinol
0.0079	Home location at assessment - north co-ordinate (rounded)
0.0072	Carotene
0.0071	Osteoporosis, osteopenia and pathological fracture
0.0069	xanthine oxidase inhibitor\|anti-gout agent
0.0069	allopurinol

NNM-Sparse-FW

Top Factor: 54 (Contribution: 0.0723)

0.0427	Whole body fat-free mass
0.0224	NSAID\|non-steroidal anti-inflammatory drug
0.0193	Leg fat mass (right)
0.0167	Usual walking pace
0.0119	Z86 Personal history of certain other diseases
0.0118	Weight
0.0100	clarithromycin
0.0099	Arm predicted mass (left)
0.0085	Whole body fat mass
0.0071	Pulse pressure, combined automated + manual reading, adjusted by medication
0.0066	Leg fat mass (left)
0.0065	lansoprazole
0.0063	aspirin
0.0063	diclofenac
0.0061	Other mental disorder

Raw Data

Top Factor: 75 (Contribution: 0.0839)

0.0341	SHBG
0.0298	Pulse rate, automated reading
0.0129	Pulse rate
0.0122	Testosterone
0.0118	COVID-19 positive (controls include untested)
0.0118	COVID-19 positive (controls include untested), only patients from centers in England
0.0113	COVID-19 positive (controls include untested)
0.0112	COVID-19 positive (controls include untested), only patients from centers in England
0.0099	COVID-19 positive (controls only COVID-19 negative)
0.0097	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0096	COVID-19 positive (controls only COVID-19 negative)
0.0090	Cystatin C
0.0090	Fasciitis
0.0089	Contracture of palmar fascia [Dupuytren's disease]
0.0088	Disorders of muscle, ligament, and fascia

Code

pan_ukb_pleiotropy(1677)

Covid-19 Positive (Controls Only Covid-19 Negative)

RPCA-IALM

Top Factor: 42 (Contribution: 0.4360)

0.0801	COVID-19 positive (controls include untested)
0.0800	COVID-19 positive (controls include untested), only patients from centers in England
0.0792	COVID-19 positive (controls include untested)
0.0791	COVID-19 positive (controls include untested), only patients from centers in England
0.0557	COVID-19 positive (controls only COVID-19 negative)
0.0498	COVID-19 positive (controls only COVID-19 negative)
0.0135	Cholelithiasis
0.0132	Cholelithiasis and cholecystitis
0.0130	K80 Cholelithiasis
0.0094	Chronic dermatitis due to solar radiation
0.0093	L57 Skin changes due to chronic exposure to nonionising radiation
0.0082	Dermatitis due to solar radiation
0.0069	Actinic keratosis
0.0068	Breast cancer [female]
0.0066	Breast cancer

NNM-Sparse-FW

Top Factor: 47 (Contribution: 0.0847)

0.0245	Age first had sexual intercourse
0.0170	Forced expiratory volume in 1-second (FEV1), predicted
0.0135	ACE inhibitor\|anti-hypertensive
0.0126	beta-lactam antibiotic\|antibiotic
0.0115	Forced expiratory volume in 1-second (FEV1), Best measure
0.0115	Whole body fat-free mass
0.0112	Arm fat-free mass (left)
0.0096	Trunk fat percentage
0.0093	Waist circumference
0.0087	Leg predicted mass (left)
0.0085	Impedance of leg (right)
0.0081	Leg fat-free mass (left)
0.0070	Ankle spacing width
0.0069	Body fat percentage
0.0059	Cholesterol

Raw Data

Top Factor: 67 (Contribution: 0.5227)

0.0846	COVID-19 positive (controls include untested), only patients from centers in England
0.0846	COVID-19 positive (controls include untested)
0.0844	COVID-19 positive (controls include untested), only patients from centers in England
0.0843	COVID-19 positive (controls include untested)
0.0765	COVID-19 positive (controls only COVID-19 negative)
0.0720	COVID-19 positive (controls only COVID-19 negative)
0.0317	IGF-1
0.0114	Platelet distribution width
0.0088	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0069	Cystatin C
0.0047	Systolic blood pressure, manual reading
0.0044	Systolic blood pressure, manual reading, adjusted by medication
0.0040	Mean arterial pressure, manual reading
0.0038	Estimated glomerular filtration rate, serum creatinine
0.0037	Creatinine

Neuropsychiatric Disorders

Code

for z in range(52,58):
    pan_ukb_pleiotropy(z)

F05 Delirium, Not Induced By Alcohol And Other Psychoactive Substances

RPCA-IALM

Top Factor: 99 (Contribution: 0.1305)

0.0148	Cardiac arrest
0.0146	Cardiac arrest and ventricular fibrillation
0.0144	I46 Cardiac arrest
0.0130	Other disorders of pancreatic internal secretion
0.0125	Hypoglycemia
0.0122	E16 Other disorders of pancreatic internal secretion
0.0112	Obesity
0.0111	E66 Obesity
0.0104	E21 Hyperparathyroidism and other disorders of parathyroid gland
0.0104	G47 Sleep disorders
0.0103	Hyperparathyroidism
0.0101	Sleep disorders
0.0101	Overweight, obesity and other hyperalimentation
0.0090	Varicose veins of lower extremity
0.0088	Disorders of parathyroid gland

NNM-Sparse-FW

Top Factor: 28 (Contribution: 0.0542)

0.0267	Waist circumference
0.0242	Body fat percentage
0.0220	E66 Obesity
0.0212	Obesity
0.0160	Arm fat mass (left)
0.0151	Trunk fat percentage
0.0128	Leg fat percentage (left)
0.0121	Leg fat percentage (right)
0.0117	pheno 48 / pheno 49
0.0112	Disorders of lipoid metabolism
0.0108	Forced expiratory volume in 1-second (FEV1), predicted
0.0107	ACE inhibitor\|anti-hypertensive
0.0104	Triglycerides
0.0092	Overweight, obesity and other hyperalimentation
0.0091	Leg fat-free mass (right)

Raw Data

Top Factor: 33 (Contribution: 0.0945)

0.1299	Monocyte percentage
0.0755	Monocyte count
0.0237	Lymphocyte count
0.0195	Eosinophill count
0.0162	Forced expiratory volume in 1-second (FEV1), Best measure
0.0155	Eosinophill percentage
0.0154	Forced expiratory volume in 1-second (FEV1)
0.0152	Lymphocyte percentage
0.0132	HDL cholesterol
0.0119	Forced expiratory volume in 1-second (FEV1), predicted percentage
0.0116	Apolipoprotein A
0.0102	Forced vital capacity (FVC), Best measure
0.0099	Forced vital capacity (FVC)
0.0082	Non-cancer illness code, self-reported
0.0075	FEV1/FVC ratio

F10 Mental And Behavioural Disorders Due To Use Of Alcohol

RPCA-IALM

Top Factor: 94 (Contribution: 0.0704)

0.0258	Intra-ocular pressure, corneal-compensated (right)
0.0234	Intra-ocular pressure, corneal-compensated (left)
0.0195	Hypotension NOS
0.0195	I95 Hypotension
0.0191	H40 Glaucoma
0.0180	Glaucoma
0.0178	Open-angle glaucoma
0.0176	Primary open angle glaucoma
0.0155	Hypotension
0.0132	Corneal hysteresis (right)
0.0124	Intra-ocular pressure, Goldmann-correlated (right)
0.0124	Corneal hysteresis (left)
0.0111	Intra-ocular pressure, Goldmann-correlated (left)
0.0110	Inguinal hernia
0.0102	K40 Inguinal hernia

NNM-Sparse-FW

Top Factor: 32 (Contribution: 0.1297)

0.0387	Trunk fat mass
0.0221	Trunk fat-free mass
0.0160	Whole body fat mass
0.0147	NSAID\|non-steroidal anti-inflammatory drug
0.0113	Ankle spacing width
0.0108	I25 Chronic ischaemic heart disease
0.0106	Multi-site chronic pain
0.0102	Comparative height size at age 10
0.0098	Leg predicted mass (right)
0.0094	Drive faster than motorway speed limit
0.0092	Hand grip strength (left)
0.0089	ibuprofen
0.0087	Impedance of leg (right)
0.0078	Hip circumference
0.0078	Diastolic blood pressure, combined automated + manual reading

Raw Data

Top Factor: 56 (Contribution: 0.1128)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

F17 Mental And Behavioural Disorders Due To Use Of Tobacco

RPCA-IALM

Top Factor: 51 (Contribution: 0.0921)

0.0368	Albumin/Globulin ratio
0.0319	Non-albumin protein
0.0142	Lymphocyte count
0.0085	Total protein
0.0073	Lymphocyte percentage
0.0072	Albumin
0.0069	Neutrophill percentage
0.0067	Platelet count
0.0063	Past tobacco smoking
0.0062	Smoking status, ever vs never
0.0062	Forced expiratory volume in 1-second (FEV1)
0.0057	Cystitis
0.0055	Forced expiratory volume in 1-second (FEV1), Best measure
0.0053	Acute pulmonary heart disease
0.0053	Pulmonary embolism and infarction, acute

NNM-Sparse-FW

Top Factor: 5 (Contribution: 0.0615)

0.0297	Mean arterial pressure, combined automated + manual reading, adjusted by medication
0.0277	Mean arterial pressure, automated reading, adjusted by medication
0.0277	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0263	Systolic blood pressure, automated reading, adjusted by medication
0.0218	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0211	Diastolic blood pressure, automated reading, adjusted by medication
0.0198	Mean arterial pressure, combined automated + manual reading
0.0194	Systolic blood pressure, combined automated + manual reading
0.0187	Mean arterial pressure, automated reading
0.0183	Systolic blood pressure, automated reading
0.0139	Diastolic blood pressure, combined automated + manual reading
0.0137	Non-cancer illness code, self-reported
0.0127	Diastolic blood pressure, automated reading
0.0116	Pulse pressure, combined automated + manual reading, adjusted by medication
0.0109	Pulse pressure, automated reading, adjusted by medication

Raw Data

Top Factor: 38 (Contribution: 0.0717)

0.0276	Corneal resistance factor (right)
0.0261	Corneal resistance factor (left)
0.0205	Urate
0.0165	Lipoprotein A
0.0159	Red blood cell (erythrocyte) distribution width
0.0155	Intra-ocular pressure, Goldmann-correlated (left)
0.0151	Alkaline phosphatase
0.0150	Intra-ocular pressure, Goldmann-correlated (right)
0.0148	Corneal hysteresis (right)
0.0137	Corneal hysteresis (left)
0.0133	Non-cancer illness code, self-reported
0.0112	Hypothyroidism NOS
0.0111	Hypothyroidism
0.0110	E03 Other hypothyroidism
0.0106	SHBG

F31 Bipolar Affective Disorder

RPCA-IALM

Top Factor: 92 (Contribution: 0.1087)

0.0288	Varicose veins of lower extremity
0.0265	Varicose veins
0.0247	I83 Varicose veins of lower extremities
0.0180	Acquired foot deformities
0.0176	M20 Acquired deformities of fingers and toes
0.0154	Other non-epithelial cancer of skin
0.0148	C44 Other malignant neoplasms of skin
0.0143	Skin cancer
0.0118	Aortic aneurysm
0.0117	I71 Aortic aneurysm and dissection
0.0105	R06 Abnormalities of breathing
0.0103	Hallux valgus (Bunion)
0.0102	Respiratory abnormalities
0.0091	Macular degeneration (senile) of retina NOS
0.0090	Degeneration of macula and posterior pole of retina

NNM-Sparse-FW

Top Factor: 23 (Contribution: 0.0730)

0.0272	E66 Obesity
0.0271	Obesity
0.0186	Overweight, obesity and other hyperalimentation
0.0160	Body mass index (BMI)
0.0137	Ankle spacing width (right)
0.0113	Standing height
0.0086	Leg fat percentage (right)
0.0085	Ankle spacing width (left)
0.0075	Weight
0.0074	Pulse pressure, automated reading, adjusted by medication
0.0074	Pulse pressure, automated reading
0.0074	Pulse pressure, combined automated + manual reading
0.0065	proton pump inhibitor\|PPI
0.0063	Weight
0.0062	calcium channel blocker\|dihydropyridine\|anti-hypertensive

Raw Data

Top Factor: 45 (Contribution: 0.0787)

0.0188	Mean carotid IMT (intima-medial thickness) at 210 degrees
0.0180	Mean carotid IMT (intima-medial thickness) at 240 degrees
0.0177	Lipoprotein A
0.0166	Mean carotid IMT (intima-medial thickness) at 120 degrees
0.0164	Mean carotid IMT (intima-medial thickness) at 150 degrees
0.0164	Maximum carotid IMT (intima-medial thickness) at 210 degrees
0.0158	Maximum carotid IMT (intima-medial thickness) at 240 degrees
0.0155	Minimum carotid IMT (intima-medial thickness) at 210 degrees
0.0145	Minimum carotid IMT (intima-medial thickness) at 240 degrees
0.0138	Minimum carotid IMT (intima-medial thickness) at 120 degrees
0.0138	Maximum carotid IMT (intima-medial thickness) at 120 degrees
0.0136	Maximum carotid IMT (intima-medial thickness) at 150 degrees
0.0132	Minimum carotid IMT (intima-medial thickness) at 150 degrees
0.0076	Urate
0.0068	Disorders of menstruation and other abnormal bleeding from female genital tract

F32 Depressive Episode

RPCA-IALM

Top Factor: 50 (Contribution: 0.1116)

0.0225	I35 Nonrheumatic aortic valve disorders
0.0224	Nonrheumatic aortic valve disorders
0.0149	Late effects of cerebrovascular disease
0.0145	I69 Sequelae of cerebrovascular disease
0.0142	Cerebrovascular disease
0.0142	Congenital anomalies of great vessels
0.0131	Cardiac congenital anomalies
0.0123	Suicide or self-inflicted injury
0.0119	Heart valve disorders
0.0117	X61 Intentional self-poisoning by and exposure to antiepileptic, sedative-hypnotic, anti-Parkinsonism and psychotropic drugs, not elsewhere classified
0.0117	Hemiplegia
0.0115	G81 Hemiplegia
0.0114	Suicidal ideation or attempt
0.0114	T51 Toxic effect of alcohol
0.0114	Toxic effect of (non-ethyl) alcohol and petroleum and other solvents

NNM-Sparse-FW

Top Factor: 5 (Contribution: 0.0612)

0.0297	Mean arterial pressure, combined automated + manual reading, adjusted by medication
0.0277	Mean arterial pressure, automated reading, adjusted by medication
0.0277	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0263	Systolic blood pressure, automated reading, adjusted by medication
0.0218	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0211	Diastolic blood pressure, automated reading, adjusted by medication
0.0198	Mean arterial pressure, combined automated + manual reading
0.0194	Systolic blood pressure, combined automated + manual reading
0.0187	Mean arterial pressure, automated reading
0.0183	Systolic blood pressure, automated reading
0.0139	Diastolic blood pressure, combined automated + manual reading
0.0137	Non-cancer illness code, self-reported
0.0127	Diastolic blood pressure, automated reading
0.0116	Pulse pressure, combined automated + manual reading, adjusted by medication
0.0109	Pulse pressure, automated reading, adjusted by medication

Raw Data

Top Factor: 45 (Contribution: 0.0855)

0.0188	Mean carotid IMT (intima-medial thickness) at 210 degrees
0.0180	Mean carotid IMT (intima-medial thickness) at 240 degrees
0.0177	Lipoprotein A
0.0166	Mean carotid IMT (intima-medial thickness) at 120 degrees
0.0164	Mean carotid IMT (intima-medial thickness) at 150 degrees
0.0164	Maximum carotid IMT (intima-medial thickness) at 210 degrees
0.0158	Maximum carotid IMT (intima-medial thickness) at 240 degrees
0.0155	Minimum carotid IMT (intima-medial thickness) at 210 degrees
0.0145	Minimum carotid IMT (intima-medial thickness) at 240 degrees
0.0138	Minimum carotid IMT (intima-medial thickness) at 120 degrees
0.0138	Maximum carotid IMT (intima-medial thickness) at 120 degrees
0.0136	Maximum carotid IMT (intima-medial thickness) at 150 degrees
0.0132	Minimum carotid IMT (intima-medial thickness) at 150 degrees
0.0076	Urate
0.0068	Disorders of menstruation and other abnormal bleeding from female genital tract

F41 Other Anxiety Disorders

RPCA-IALM

Top Factor: 100 (Contribution: 0.0925)

0.0203	Varicose veins of lower extremity
0.0185	Varicose veins
0.0172	I83 Varicose veins of lower extremities
0.0169	Indirect bilirubin
0.0165	Total bilirubin
0.0130	Direct bilirubin
0.0102	Bacterial pneumonia
0.0102	Psoriasis
0.0099	Pneumococcal pneumonia
0.0097	Monocyte percentage
0.0096	L40 Psoriasis
0.0095	Pneumonia
0.0092	J18 Pneumonia, organism unspecified
0.0092	Psoriasis and related disorders
0.0078	Cardiac arrest

NNM-Sparse-FW

Top Factor: 93 (Contribution: 0.0847)

0.0244	Impedance of arm (right)
0.0191	Trunk fat mass
0.0179	E11 Non-insulin-dependent diabetes mellitus
0.0148	Impedance of leg (right)
0.0123	Type 2 diabetes
0.0104	Leg fat-free mass (left)
0.0102	Leg fat mass (left)
0.0100	Leg fat mass (right)
0.0100	doxycycline
0.0100	Whole body water mass
0.0090	Body mass index (BMI)
0.0087	Trunk fat percentage
0.0086	tetracycline antibiotic\|antibiotic
0.0081	ramipril
0.0077	Cystatin C

Raw Data

Top Factor: 53 (Contribution: 0.0682)

0.0102	Corneal resistance factor (right)
0.0096	X61 Intentional self-poisoning by and exposure to antiepileptic, sedative-hypnotic, anti-Parkinsonism and psychotropic drugs, not elsewhere classified
0.0091	Corneal resistance factor (left)
0.0090	Poisoning by psychotropic agents
0.0085	SHBG
0.0083	T43 Poisoning by psychotropic drugs, not elsewhere classified
0.0083	Suicide or self-inflicted injury
0.0080	Suicidal ideation or attempt
0.0075	Home location - north co-ordinate (rounded)
0.0075	Home location at assessment - north co-ordinate (rounded)
0.0074	Toxic effect of (non-ethyl) alcohol and petroleum and other solvents
0.0073	T51 Toxic effect of alcohol
0.0073	T39 Poisoning by nonopioid analgesics, antipyretics and antirheumatics
0.0073	Corneal hysteresis (right)
0.0072	X60 Intentional self-poisoning by and exposure to nonopioid analgesics, antipyretics and antirheumatics

Code

for z in range(520,538):
    pan_ukb_pleiotropy(z)

Other Mental Disorder

RPCA-IALM

Top Factor: 6 (Contribution: 0.1623)

0.0290	Trunk fat percentage
0.0231	Body fat percentage
0.0229	Impedance of whole body
0.0226	Impedance of arm (right)
0.0224	Impedance of arm (left)
0.0194	Trunk fat mass
0.0155	Arm fat percentage (left)
0.0154	Whole body fat mass
0.0153	Arm fat percentage (right)
0.0139	Leg fat percentage (right)
0.0133	Leg fat percentage (left)
0.0132	Impedance of leg (left)
0.0129	Impedance of leg (right)
0.0090	Leg fat mass (right)
0.0088	Arm fat mass (left)

NNM-Sparse-FW

Top Factor: 82 (Contribution: 0.0722)

0.0312	Body mass index (BMI)
0.0297	Leg predicted mass (left)
0.0226	Leg fat percentage (left)
0.0159	Arm fat mass (left)
0.0128	Body mass index (BMI)
0.0097	Whole body fat mass
0.0094	Diastolic blood pressure, automated reading, adjusted by medication
0.0088	Hand grip strength (left)
0.0082	aspirin
0.0082	Arm fat-free mass (left)
0.0081	SHBG
0.0073	Treatment/medication code
0.0072	I25 Chronic ischaemic heart disease
0.0069	corticosteroid
0.0068	C-reactive protein

Raw Data

Top Factor: 10 (Contribution: 0.1058)

0.0384	High light scatter reticulocyte percentage
0.0375	Mean corpuscular haemoglobin
0.0339	Mean corpuscular volume
0.0326	High light scatter reticulocyte count
0.0324	Reticulocyte percentage
0.0254	Reticulocyte count
0.0235	Impedance of whole body
0.0212	Impedance of arm (right)
0.0203	Impedance of arm (left)
0.0188	Immature reticulocyte fraction
0.0176	Impedance of leg (left)
0.0172	Impedance of leg (right)
0.0145	Trunk fat percentage
0.0140	Red blood cell (erythrocyte) distribution width
0.0121	Standing height

Substance Addiction And Disorders

RPCA-IALM

Top Factor: 94 (Contribution: 0.0746)

0.0258	Intra-ocular pressure, corneal-compensated (right)
0.0234	Intra-ocular pressure, corneal-compensated (left)
0.0195	Hypotension NOS
0.0195	I95 Hypotension
0.0191	H40 Glaucoma
0.0180	Glaucoma
0.0178	Open-angle glaucoma
0.0176	Primary open angle glaucoma
0.0155	Hypotension
0.0132	Corneal hysteresis (right)
0.0124	Intra-ocular pressure, Goldmann-correlated (right)
0.0124	Corneal hysteresis (left)
0.0111	Intra-ocular pressure, Goldmann-correlated (left)
0.0110	Inguinal hernia
0.0102	K40 Inguinal hernia

NNM-Sparse-FW

Top Factor: 32 (Contribution: 0.0623)

0.0387	Trunk fat mass
0.0221	Trunk fat-free mass
0.0160	Whole body fat mass
0.0147	NSAID\|non-steroidal anti-inflammatory drug
0.0113	Ankle spacing width
0.0108	I25 Chronic ischaemic heart disease
0.0106	Multi-site chronic pain
0.0102	Comparative height size at age 10
0.0098	Leg predicted mass (right)
0.0094	Drive faster than motorway speed limit
0.0092	Hand grip strength (left)
0.0089	ibuprofen
0.0087	Impedance of leg (right)
0.0078	Hip circumference
0.0078	Diastolic blood pressure, combined automated + manual reading

Raw Data

Top Factor: 56 (Contribution: 0.1156)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

Alcohol-Related Disorders

RPCA-IALM

Top Factor: 57 (Contribution: 0.0858)

0.0175	J44 Other chronic obstructive pulmonary disease
0.0170	Obstructive chronic bronchitis
0.0160	Chronic bronchitis
0.0132	Pulmonary embolism and infarction, acute
0.0132	Acute pulmonary heart disease
0.0130	Chronic airway obstruction
0.0121	I26 Pulmonary embolism
0.0113	HDL cholesterol
0.0105	Apolipoprotein A
0.0093	Total thigh muscle volume
0.0082	Pulmonary heart disease
0.0075	Alcohol intake frequency.
0.0073	Posterior thigh lean muscle volume (right)
0.0072	Posterior thigh lean muscle volume (left)
0.0068	K57 Diverticular disease of intestine

NNM-Sparse-FW

Top Factor: 5 (Contribution: 0.0513)

0.0297	Mean arterial pressure, combined automated + manual reading, adjusted by medication
0.0277	Mean arterial pressure, automated reading, adjusted by medication
0.0277	Systolic blood pressure, combined automated + manual reading, adjusted by medication
0.0263	Systolic blood pressure, automated reading, adjusted by medication
0.0218	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0211	Diastolic blood pressure, automated reading, adjusted by medication
0.0198	Mean arterial pressure, combined automated + manual reading
0.0194	Systolic blood pressure, combined automated + manual reading
0.0187	Mean arterial pressure, automated reading
0.0183	Systolic blood pressure, automated reading
0.0139	Diastolic blood pressure, combined automated + manual reading
0.0137	Non-cancer illness code, self-reported
0.0127	Diastolic blood pressure, automated reading
0.0116	Pulse pressure, combined automated + manual reading, adjusted by medication
0.0109	Pulse pressure, automated reading, adjusted by medication

Raw Data

Top Factor: 56 (Contribution: 0.1049)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

Alcoholism

RPCA-IALM

Top Factor: 94 (Contribution: 0.0867)

0.0258	Intra-ocular pressure, corneal-compensated (right)
0.0234	Intra-ocular pressure, corneal-compensated (left)
0.0195	Hypotension NOS
0.0195	I95 Hypotension
0.0191	H40 Glaucoma
0.0180	Glaucoma
0.0178	Open-angle glaucoma
0.0176	Primary open angle glaucoma
0.0155	Hypotension
0.0132	Corneal hysteresis (right)
0.0124	Intra-ocular pressure, Goldmann-correlated (right)
0.0124	Corneal hysteresis (left)
0.0111	Intra-ocular pressure, Goldmann-correlated (left)
0.0110	Inguinal hernia
0.0102	K40 Inguinal hernia

NNM-Sparse-FW

Top Factor: 15 (Contribution: 0.0573)

0.0670	Essential hypertension
0.0596	Hypertension
0.0278	E78 Disorders of lipoprotein metabolism and other lipidaemias
0.0271	Disorders of lipoid metabolism
0.0265	Hypercholesterolemia
0.0256	Hyperlipidemia
0.0252	Ischemic Heart Disease
0.0197	Other chronic ischemic heart disease, unspecified
0.0174	I25 Chronic ischaemic heart disease
0.0138	antipyretic
0.0138	paracetamol
0.0134	opioid analgesic\|antipyretic
0.0130	Angina pectoris
0.0111	E11 Non-insulin-dependent diabetes mellitus
0.0100	Leg fat mass (left)

Raw Data

Top Factor: 56 (Contribution: 0.0766)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

Alcoholic Liver Damage

RPCA-IALM

Top Factor: 94 (Contribution: 0.0981)

0.0258	Intra-ocular pressure, corneal-compensated (right)
0.0234	Intra-ocular pressure, corneal-compensated (left)
0.0195	Hypotension NOS
0.0195	I95 Hypotension
0.0191	H40 Glaucoma
0.0180	Glaucoma
0.0178	Open-angle glaucoma
0.0176	Primary open angle glaucoma
0.0155	Hypotension
0.0132	Corneal hysteresis (right)
0.0124	Intra-ocular pressure, Goldmann-correlated (right)
0.0124	Corneal hysteresis (left)
0.0111	Intra-ocular pressure, Goldmann-correlated (left)
0.0110	Inguinal hernia
0.0102	K40 Inguinal hernia

NNM-Sparse-FW

Top Factor: 88 (Contribution: 0.0513)

0.0319	Whole body fat-free mass
0.0251	Leg fat percentage (right)
0.0194	Hand grip strength (left)
0.0120	Leg predicted mass (right)
0.0118	Forced vital capacity (FVC), Best measure
0.0110	codine/paracetamol
0.0103	Arm fat-free mass (right)
0.0099	Mean arterial pressure, automated reading
0.0096	Trunk fat-free mass
0.0096	Peak expiratory flow (PEF)
0.0092	Trunk predicted mass
0.0090	Basal metabolic rate
0.0089	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0071	Arm fat mass (left)
0.0069	Age completed full time education

Raw Data

Top Factor: 89 (Contribution: 0.1356)

0.0327	Genital prolapse
0.0325	Prolapse of vaginal walls
0.0322	N81 Female genital prolapse
0.0185	Uterine/Uterovaginal prolapse
0.0143	Pulse rate, automated reading
0.0115	C-reactive protein
0.0084	Other vitamin B12 deficiency anemia
0.0084	Megaloblastic anemia
0.0084	Other deficiency anemia
0.0084	D51 Vitamin B12 deficiency anaemia
0.0077	Chronic liver disease and cirrhosis
0.0076	Pulse rate
0.0074	Gamma glutamyltransferase
0.0073	K76 Other diseases of liver
0.0072	Other disorders of liver

Tobacco Use Disorder

RPCA-IALM

Top Factor: 51 (Contribution: 0.0944)

0.0368	Albumin/Globulin ratio
0.0319	Non-albumin protein
0.0142	Lymphocyte count
0.0085	Total protein
0.0073	Lymphocyte percentage
0.0072	Albumin
0.0069	Neutrophill percentage
0.0067	Platelet count
0.0063	Past tobacco smoking
0.0062	Smoking status, ever vs never
0.0062	Forced expiratory volume in 1-second (FEV1)
0.0057	Cystitis
0.0055	Forced expiratory volume in 1-second (FEV1), Best measure
0.0053	Acute pulmonary heart disease
0.0053	Pulmonary embolism and infarction, acute

NNM-Sparse-FW

Top Factor: 42 (Contribution: 0.0911)

0.0228	Leg fat mass (right)
0.0227	Arm predicted mass (left)
0.0162	Ankle spacing width (right)
0.0147	Hip circumference
0.0114	selective serotonin re-uptake inhibitor\|SSRI
0.0110	Body mass index (BMI)
0.0108	Trunk predicted mass
0.0094	proton pump inhibitor\|PPI
0.0091	beta-lactam antibiotic\|antibiotic
0.0087	Impedance of leg (left)
0.0085	Sitting height
0.0073	Heel bone mineral density (BMD) T-score, automated (left)
0.0073	Heel quantitative ultrasound index (QUI), direct entry (left)
0.0071	Hypertension
0.0071	Body fat percentage

Raw Data

Top Factor: 38 (Contribution: 0.0719)

0.0276	Corneal resistance factor (right)
0.0261	Corneal resistance factor (left)
0.0205	Urate
0.0165	Lipoprotein A
0.0159	Red blood cell (erythrocyte) distribution width
0.0155	Intra-ocular pressure, Goldmann-correlated (left)
0.0151	Alkaline phosphatase
0.0150	Intra-ocular pressure, Goldmann-correlated (right)
0.0148	Corneal hysteresis (right)
0.0137	Corneal hysteresis (left)
0.0133	Non-cancer illness code, self-reported
0.0112	Hypothyroidism NOS
0.0111	Hypothyroidism
0.0110	E03 Other hypothyroidism
0.0106	SHBG

Sleep Disorders

RPCA-IALM

Top Factor: 86 (Contribution: 0.1209)

0.0469	Acquired foot deformities
0.0468	M20 Acquired deformities of fingers and toes
0.0290	Hemoptysis
0.0286	R04 Haemorrhage from respiratory passages
0.0275	Obesity
0.0272	E66 Obesity
0.0272	Hallux valgus (Bunion)
0.0253	Acquired toe deformities
0.0248	Abnormal sputum
0.0247	Overweight, obesity and other hyperalimentation
0.0123	G47 Sleep disorders
0.0119	Sleep disorders
0.0111	Hammer toe (acquired)
0.0110	Epistaxis or throat hemorrhage
0.0095	Prostatitis

NNM-Sparse-FW

Top Factor: 4 (Contribution: 0.0595)

0.1274	Standing height
0.0721	Sitting height
0.0263	Seated height
0.0192	Comparative height size at age 10
0.0190	Trunk fat-free mass
0.0189	Trunk predicted mass
0.0134	Whole body fat-free mass
0.0117	Whole body water mass
0.0114	Waist circumference
0.0112	Leg fat mass (left)
0.0112	Arm fat mass (right)
0.0107	Leg fat mass (right)
0.0101	Arm fat mass (left)
0.0099	E66 Obesity
0.0099	Obesity

Raw Data

Top Factor: 91 (Contribution: 0.1044)

0.0136	Aspartate aminotransferase
0.0125	Platelet distribution width
0.0112	Alanine aminotransferase
0.0084	Inflammatory bowel disease and other gastroenteritis and colitis
0.0074	Spherical power (right)
0.0070	Genital prolapse
0.0070	Prolapse of vaginal walls
0.0069	Spherical power (left)
0.0068	N81 Female genital prolapse
0.0068	Open wounds of head; neck; and trunk
0.0063	C79 Secondary malignant neoplasm of other sites
0.0061	E87 Other disorders of fluid, electrolyte and acid-base balance
0.0061	Ulcerative colitis
0.0061	Electrolyte imbalance
0.0061	I77 Other disorders of arteries and arterioles

Sleep Apnea

RPCA-IALM

Top Factor: 86 (Contribution: 0.1234)

0.0469	Acquired foot deformities
0.0468	M20 Acquired deformities of fingers and toes
0.0290	Hemoptysis
0.0286	R04 Haemorrhage from respiratory passages
0.0275	Obesity
0.0272	E66 Obesity
0.0272	Hallux valgus (Bunion)
0.0253	Acquired toe deformities
0.0248	Abnormal sputum
0.0247	Overweight, obesity and other hyperalimentation
0.0123	G47 Sleep disorders
0.0119	Sleep disorders
0.0111	Hammer toe (acquired)
0.0110	Epistaxis or throat hemorrhage
0.0095	Prostatitis

NNM-Sparse-FW

Top Factor: 99 (Contribution: 0.0651)

0.0275	Impedance of arm (right)
0.0160	proton pump inhibitor\|PPI
0.0146	Whole body fat-free mass
0.0119	NSAID\|non-steroidal anti-inflammatory drug
0.0113	Leg fat percentage (left)
0.0110	Forced expiratory volume in 1-second (FEV1), predicted
0.0089	corticosteroid
0.0087	anti-fungal
0.0078	Impedance of whole body
0.0077	Renal failure
0.0076	Ankle spacing width
0.0075	Waist circumference
0.0073	Hand grip strength (right)
0.0072	Mean arterial pressure, combined automated + manual reading
0.0069	doxycycline

Raw Data

Top Factor: 91 (Contribution: 0.1055)

0.0136	Aspartate aminotransferase
0.0125	Platelet distribution width
0.0112	Alanine aminotransferase
0.0084	Inflammatory bowel disease and other gastroenteritis and colitis
0.0074	Spherical power (right)
0.0070	Genital prolapse
0.0070	Prolapse of vaginal walls
0.0069	Spherical power (left)
0.0068	N81 Female genital prolapse
0.0068	Open wounds of head; neck; and trunk
0.0063	C79 Secondary malignant neoplasm of other sites
0.0061	E87 Other disorders of fluid, electrolyte and acid-base balance
0.0061	Ulcerative colitis
0.0061	Electrolyte imbalance
0.0061	I77 Other disorders of arteries and arterioles

Other Cerebral Degenerations

RPCA-IALM

Top Factor: 32 (Contribution: 0.0892)

0.0219	Mean carotid IMT (intima-medial thickness) at 210 degrees
0.0207	Mean carotid IMT (intima-medial thickness) at 240 degrees
0.0195	Mean carotid IMT (intima-medial thickness) at 120 degrees
0.0187	Mean carotid IMT (intima-medial thickness) at 150 degrees
0.0165	Maximum carotid IMT (intima-medial thickness) at 210 degrees
0.0158	Maximum carotid IMT (intima-medial thickness) at 240 degrees
0.0151	Minimum carotid IMT (intima-medial thickness) at 210 degrees
0.0139	Minimum carotid IMT (intima-medial thickness) at 240 degrees
0.0138	Maximum carotid IMT (intima-medial thickness) at 120 degrees
0.0138	Minimum carotid IMT (intima-medial thickness) at 120 degrees
0.0133	Minimum carotid IMT (intima-medial thickness) at 150 degrees
0.0132	Maximum carotid IMT (intima-medial thickness) at 150 degrees
0.0097	Heart valve disorders
0.0093	Neutrophill percentage
0.0088	Nonrheumatic aortic valve disorders

NNM-Sparse-FW

Top Factor: 76 (Contribution: 0.1215)

0.0407	Arm fat-free mass (right)
0.0200	corticosteroid
0.0140	Arm fat-free mass (left)
0.0105	Ankle spacing width (left)
0.0103	Whole body fat-free mass
0.0098	Coronary atherosclerosis
0.0097	Body fat percentage
0.0096	clotrimazole
0.0096	Arm predicted mass (right)
0.0093	Leg predicted mass (right)
0.0080	Trunk fat mass
0.0079	Body mass index (BMI)
0.0072	Forced vital capacity (FVC), Best measure
0.0068	Whole body water mass
0.0067	Arm fat percentage (left)

Raw Data

Top Factor: 61 (Contribution: 0.1172)

0.0324	Heel bone mineral density (BMD)
0.0322	Heel bone mineral density (BMD) T-score, automated
0.0322	Heel quantitative ultrasound index (QUI), direct entry
0.0258	Heel Broadband ultrasound attenuation, direct entry
0.0139	Urate
0.0119	Heel bone mineral density (BMD) T-score, automated (left)
0.0119	Heel quantitative ultrasound index (QUI), direct entry (left)
0.0119	Heel broadband ultrasound attenuation (left)
0.0116	Heel bone mineral density (BMD) (left)
0.0115	Heel bone mineral density (BMD) T-score, automated (right)
0.0115	Heel quantitative ultrasound index (QUI), direct entry (right)
0.0115	Heel broadband ultrasound attenuation (right)
0.0114	Heel bone mineral density (BMD) (right)
0.0103	Cerebrovascular disease
0.0102	Creatinine

Parkinson’s Disease

RPCA-IALM

Top Factor: 97 (Contribution: 0.0888)

0.0441	Psoriasis
0.0425	L40 Psoriasis
0.0403	Psoriasis and related disorders
0.0187	Cardiac arrest
0.0184	Cardiac arrest and ventricular fibrillation
0.0181	I46 Cardiac arrest
0.0117	K90 Intestinal malabsorption
0.0114	Intestinal malabsorption (non-celiac)
0.0109	Obesity
0.0108	E66 Obesity
0.0097	Overweight, obesity and other hyperalimentation
0.0095	Aortic aneurysm
0.0094	I71 Aortic aneurysm and dissection
0.0090	Celiac disease
0.0085	Noninflammatory disorders of ovary, fallopian tube, and broad ligament

NNM-Sparse-FW

Top Factor: 70 (Contribution: 0.0852)

0.0262	Trunk fat percentage
0.0240	Whole body fat-free mass
0.0207	Leg predicted mass (left)
0.0201	Arm fat-free mass (left)
0.0172	Leg fat percentage (left)
0.0147	Leg fat mass (right)
0.0105	Leg fat mass (left)
0.0083	NSAID\|non-steroidal anti-inflammatory drug
0.0079	Usual walking pace
0.0078	proton pump inhibitor\|PPI
0.0073	Impedance of leg (left)
0.0071	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0065	Arm fat mass (right)
0.0061	Diastolic blood pressure, combined automated + manual reading, adjusted by medication
0.0059	codine/paracetamol

Raw Data

Top Factor: 92 (Contribution: 0.1208)

0.0149	Urinary calculus
0.0149	N20 Calculus of kidney and ureter
0.0147	Maximum heart rate during fitness test
0.0146	ECG, load
0.0146	Maximum workload during fitness test
0.0139	Pulse rate, automated reading
0.0138	ECG, heart rate
0.0130	ECG, number of stages in a phase
0.0126	Number of trend entries
0.0117	ECG, phase time
0.0110	Calculus of ureter
0.0102	Processed meat intake
0.0101	Calculus of kidney
0.0088	Beef intake
0.0080	Lamb/mutton intake

Extrapyramidal Disease And Abnormal Movement Disorders

RPCA-IALM

Top Factor: 68 (Contribution: 0.0752)

0.0221	Prolapse of vaginal walls
0.0212	Genital prolapse
0.0210	N81 Female genital prolapse
0.0119	Platelet count
0.0116	Albumin
0.0114	Primary/intrinsic cardiomyopathies
0.0114	I42 Cardiomyopathy
0.0106	Cardiomyopathy
0.0097	Saturated fat
0.0097	Lymphocyte count
0.0096	Eosinophill percentage
0.0089	Fat
0.0085	Polyp of corpus uteri
0.0085	Total thigh muscle volume
0.0084	N84 Polyp of female genital tract

NNM-Sparse-FW

Top Factor: 95 (Contribution: 0.0865)

0.0408	Trunk fat-free mass
0.0198	Trunk predicted mass
0.0149	Leg fat mass (right)
0.0139	Leg fat-free mass (right)
0.0126	tetracycline antibiotic\|antibiotic
0.0112	E66 Obesity
0.0111	Impedance of leg (left)
0.0093	Reticulocyte percentage
0.0091	Body mass index (BMI)
0.0090	Arm predicted mass (right)
0.0087	selective serotonin re-uptake inhibitor\|SSRI
0.0086	Non-cancer illness code, self-reported
0.0084	simvastatin
0.0078	Impedance of whole body
0.0072	High light scatter reticulocyte count

Raw Data

Top Factor: 95 (Contribution: 0.0773)

0.0487	Sebaceous cyst
0.0484	Diseases of sebaceous glands
0.0473	L72 Follicular cysts of skin and subcutaneous tissue
0.0373	Diseases of hair and hair follicles
0.0088	IGF-1
0.0086	Acquired foot deformities
0.0084	M20 Acquired deformities of fingers and toes
0.0078	Sodium in urine
0.0071	Acquired toe deformities
0.0068	FEV1/FVC ratio
0.0067	Urea
0.0067	Cancer of bladder
0.0065	C67 Malignant neoplasm of bladder
0.0065	Malignant neoplasm of bladder
0.0064	Cystitis

Degenerative Disease Of The Spinal Cord

RPCA-IALM

Top Factor: 62 (Contribution: 0.0881)

0.0405	Other vitamin B12 deficiency anemia
0.0405	D51 Vitamin B12 deficiency anaemia
0.0340	Megaloblastic anemia
0.0315	Other deficiency anemia
0.0202	Intervertebral disc disorders
0.0195	G55 Nerve root and plexus compressions in diseases classified elsewhere
0.0189	Other and unspecified disc disorder
0.0181	Nerve root and plexus disorders
0.0163	Contracture of palmar fascia [Dupuytren's disease]
0.0157	Disorders of muscle, ligament, and fascia
0.0146	Fasciitis
0.0117	M51 Other intervertebral disk disorders
0.0103	M72 Fibroblastic disorders
0.0097	Non-albumin protein
0.0084	Eosinophill percentage

NNM-Sparse-FW

Top Factor: 98 (Contribution: 0.0866)

0.0240	Leg predicted mass (right)
0.0211	Arm fat percentage (right)
0.0197	Waist circumference
0.0146	Impedance of leg (left)
0.0115	Leg fat-free mass (left)
0.0113	Arm fat-free mass (left)
0.0112	Overall health rating
0.0108	opioid analgesic\|antipyretic
0.0105	Leg fat mass (right)
0.0101	Arm fat percentage (left)
0.0089	antispasmodic
0.0088	Hip circumference
0.0085	Trunk predicted mass
0.0084	Arm predicted mass (left)
0.0082	Whole body fat-free mass

Raw Data

Top Factor: 68 (Contribution: 0.0984)

0.0098	Corneal hysteresis (right)
0.0095	Corneal hysteresis (left)
0.0094	Intra-ocular pressure, corneal-compensated (left)
0.0092	I35 Nonrheumatic aortic valve disorders
0.0092	Intra-ocular pressure, corneal-compensated (right)
0.0091	Nonrheumatic aortic valve disorders
0.0079	Alkaline phosphatase
0.0075	Congenital anomalies of great vessels
0.0075	Intervertebral disc disorders
0.0072	3mm strong meridian angle (left)
0.0072	Osteoporosis
0.0072	Osteoporosis NOS
0.0071	Aortic aneurysm
0.0070	I71 Aortic aneurysm and dissection
0.0070	Other and unspecified disc disorder

Multiple Sclerosis

RPCA-IALM

Top Factor: 74 (Contribution: 0.0911)

0.0203	Inflammatory bowel disease and other gastroenteritis and colitis
0.0168	Ulcerative colitis
0.0164	K51 Ulcerative colitis
0.0120	Albumin
0.0119	Dental caries
0.0117	Total protein
0.0113	K02 Dental caries
0.0112	Diseases of hard tissues of teeth
0.0107	Aortic aneurysm
0.0103	I71 Aortic aneurysm and dissection
0.0096	Appendicitis
0.0095	Acute appendicitis
0.0093	Regional enteritis
0.0092	K50 Crohn's disease [regional enteritis]
0.0090	Platelet count

NNM-Sparse-FW

Top Factor: 65 (Contribution: 0.0684)

0.0205	Leg fat mass (left)
0.0158	Forced expiratory volume in 1-second (FEV1), predicted
0.0104	Impedance of whole body
0.0095	flucloxacillin
0.0082	Arm predicted mass (right)
0.0077	Arm fat percentage (left)
0.0076	Essential hypertension
0.0073	Overweight, obesity and other hyperalimentation
0.0073	Basal metabolic rate
0.0073	Sitting height
0.0073	bendroflumethiazide
0.0070	Forced expiratory volume in 1-second (FEV1), Best measure
0.0067	Trunk fat mass
0.0067	Leg fat-free mass (left)
0.0065	atorvastatin

Raw Data

Top Factor: 77 (Contribution: 0.0818)

0.0424	Contracture of palmar fascia [Dupuytren's disease]
0.0416	Disorders of muscle, ligament, and fascia
0.0413	Fasciitis
0.0344	M72 Fibroblastic disorders
0.0276	ECG, number of stages in a phase
0.0267	ECG, load
0.0264	Maximum workload during fitness test
0.0229	Number of trend entries
0.0226	ECG, phase time
0.0129	Corneal hysteresis (left)
0.0129	Corneal hysteresis (right)
0.0118	Duration of fitness test
0.0077	Getting up in morning
0.0075	Corneal resistance factor (left)
0.0073	Corneal resistance factor (right)

Other Headache Syndromes

RPCA-IALM

Top Factor: 92 (Contribution: 0.0529)

0.0288	Varicose veins of lower extremity
0.0265	Varicose veins
0.0247	I83 Varicose veins of lower extremities
0.0180	Acquired foot deformities
0.0176	M20 Acquired deformities of fingers and toes
0.0154	Other non-epithelial cancer of skin
0.0148	C44 Other malignant neoplasms of skin
0.0143	Skin cancer
0.0118	Aortic aneurysm
0.0117	I71 Aortic aneurysm and dissection
0.0105	R06 Abnormalities of breathing
0.0103	Hallux valgus (Bunion)
0.0102	Respiratory abnormalities
0.0091	Macular degeneration (senile) of retina NOS
0.0090	Degeneration of macula and posterior pole of retina

NNM-Sparse-FW

Top Factor: 48 (Contribution: 0.0612)

0.0247	Weight
0.0190	Whole body water mass
0.0134	Trunk fat mass
0.0132	Age at first live birth
0.0128	Weight
0.0123	Arm fat-free mass (left)
0.0119	Overweight, obesity and other hyperalimentation
0.0112	Body mass index (BMI)
0.0108	Leg fat percentage (right)
0.0089	Hip circumference
0.0088	Leg fat-free mass (right)
0.0081	Trunk predicted mass
0.0064	aspirin
0.0064	Leg fat-free mass (left)
0.0063	sodium alginate / potassium bicarbonate

Raw Data

Top Factor: 56 (Contribution: 0.1011)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

Migraine

RPCA-IALM

Top Factor: 80 (Contribution: 0.0772)

0.0312	Appendicitis
0.0307	Acute appendicitis
0.0287	Appendiceal conditions
0.0284	K35 Acute appendicitis
0.0208	Sebaceous cyst
0.0203	Diseases of sebaceous glands
0.0186	L72 Follicular cysts of skin and subcutaneous tissue
0.0140	Contracture of palmar fascia [Dupuytren's disease]
0.0134	Disorders of muscle, ligament, and fascia
0.0133	Iron deficiency anemias, unspecified or not due to blood loss
0.0133	Iron deficiency anemias
0.0121	Fasciitis
0.0118	D50 Iron deficiency anaemia
0.0115	Home location - north co-ordinate (rounded)
0.0113	Home location at assessment - north co-ordinate (rounded)

NNM-Sparse-FW

Top Factor: 100 (Contribution: 0.0520)

0.0150	Impedance of arm (left)
0.0145	Apolipoprotein A
0.0134	Overweight, obesity and other hyperalimentation
0.0119	Hand grip strength (right)
0.0117	Weight
0.0108	corticosteroid
0.0107	Impedance of leg (left)
0.0102	Leg predicted mass (right)
0.0096	Basal metabolic rate
0.0096	Maximum workload during fitness test
0.0094	Forced vital capacity (FVC)
0.0077	Ankle spacing width
0.0075	antispasmodic
0.0070	Peak expiratory flow (PEF)
0.0064	Renal failure

Raw Data

Top Factor: 56 (Contribution: 0.0774)

0.0227	Alkaline phosphatase
0.0134	Red blood cell (erythrocyte) distribution width
0.0104	Albumin
0.0079	Alanine aminotransferase
0.0077	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0072	Other disorders of bladder
0.0071	Aspartate aminotransferase
0.0071	Other retinal disorders
0.0065	Cystatin C
0.0064	N32 Other disorders of bladder
0.0062	Calcium
0.0061	Gamma glutamyltransferase
0.0057	Diabetic retinopathy
0.0057	Hereditary retinal dystrophies
0.0057	H36 Retinal disorders in diseases classified elsewhere

Hemiplegia

RPCA-IALM

Top Factor: 50 (Contribution: 0.1700)

0.0225	I35 Nonrheumatic aortic valve disorders
0.0224	Nonrheumatic aortic valve disorders
0.0149	Late effects of cerebrovascular disease
0.0145	I69 Sequelae of cerebrovascular disease
0.0142	Cerebrovascular disease
0.0142	Congenital anomalies of great vessels
0.0131	Cardiac congenital anomalies
0.0123	Suicide or self-inflicted injury
0.0119	Heart valve disorders
0.0117	X61 Intentional self-poisoning by and exposure to antiepileptic, sedative-hypnotic, anti-Parkinsonism and psychotropic drugs, not elsewhere classified
0.0117	Hemiplegia
0.0115	G81 Hemiplegia
0.0114	Suicidal ideation or attempt
0.0114	T51 Toxic effect of alcohol
0.0114	Toxic effect of (non-ethyl) alcohol and petroleum and other solvents

NNM-Sparse-FW

Top Factor: 25 (Contribution: 0.0582)

0.0297	Obesity
0.0293	E66 Obesity
0.0172	Overweight, obesity and other hyperalimentation
0.0159	Leg fat mass (left)
0.0155	Pulse pressure, automated reading, adjusted by medication
0.0134	Estimated glomerular filtration rate, serum creatinine + cystain C
0.0128	Seating box height
0.0127	Pulse pressure, combined automated + manual reading, adjusted by medication
0.0127	Coronary atherosclerosis
0.0118	Pulse pressure, combined automated + manual reading
0.0106	Sitting height
0.0105	HMG CoA reductase inhibitor\|statin
0.0102	lansoprazole
0.0099	Trunk fat percentage
0.0095	Whole body fat mass

Raw Data

Top Factor: 64 (Contribution: 0.2000)

0.0165	Cerebrovascular disease
0.0127	SHBG
0.0124	Acute pulmonary heart disease
0.0124	Pulmonary embolism and infarction, acute
0.0123	I26 Pulmonary embolism
0.0113	Pulmonary heart disease
0.0104	Breast cancer [female]
0.0103	Late effects of cerebrovascular disease
0.0103	Breast cancer
0.0100	I69 Sequelae of cerebrovascular disease
0.0099	Cerebral ischemia
0.0097	Malignant neoplasm of female breast
0.0095	C50 Malignant neoplasm of breast
0.0093	Hemiplegia
0.0092	Occlusion of cerebral arteries

Epilepsy, Recurrent Seizures, Convulsions

RPCA-IALM

Top Factor: 98 (Contribution: 0.0502)

0.0171	Platelet count
0.0121	Eosinophill count
0.0101	Polyp of corpus uteri
0.0099	R06 Abnormalities of breathing
0.0098	N84 Polyp of female genital tract
0.0097	Respiratory abnormalities
0.0093	Polyp of female genital organs
0.0091	I71 Aortic aneurysm and dissection
0.0089	Aortic aneurysm
0.0083	Platelet crit
0.0083	Eosinophill percentage
0.0074	Bundle branch block
0.0071	Purpura and other hemorrhagic conditions
0.0070	Cardiac conduction disorders
0.0070	D69 Purpura and other haemorrhagic conditions

NNM-Sparse-FW

Top Factor: 96 (Contribution: 0.1166)

0.0249	Ankle spacing width (right)
0.0187	Impedance of leg (left)
0.0154	proton pump inhibitor\|PPI
0.0153	Angina pectoris
0.0143	Whole body fat-free mass
0.0134	Non-cancer illness code, self-reported
0.0127	benzodiazepine\|sedative\|anxiety
0.0115	Ischemic Heart Disease
0.0111	Sitting height
0.0088	Leg predicted mass (left)
0.0088	Seated height
0.0085	Leg fat mass (left)
0.0084	Peak expiratory flow (PEF)
0.0072	Arm predicted mass (right)
0.0070	Age at first live birth

Raw Data

Top Factor: 64 (Contribution: 0.1090)

0.0165	Cerebrovascular disease
0.0127	SHBG
0.0124	Acute pulmonary heart disease
0.0124	Pulmonary embolism and infarction, acute
0.0123	I26 Pulmonary embolism
0.0113	Pulmonary heart disease
0.0104	Breast cancer [female]
0.0103	Late effects of cerebrovascular disease
0.0103	Breast cancer
0.0100	I69 Sequelae of cerebrovascular disease
0.0099	Cerebral ischemia
0.0097	Malignant neoplasm of female breast
0.0095	C50 Malignant neoplasm of breast
0.0093	Hemiplegia
0.0092	Occlusion of cerebral arteries

Epilepsy

RPCA-IALM

Top Factor: 98 (Contribution: 0.0738)

0.0171	Platelet count
0.0121	Eosinophill count
0.0101	Polyp of corpus uteri
0.0099	R06 Abnormalities of breathing
0.0098	N84 Polyp of female genital tract
0.0097	Respiratory abnormalities
0.0093	Polyp of female genital organs
0.0091	I71 Aortic aneurysm and dissection
0.0089	Aortic aneurysm
0.0083	Platelet crit
0.0083	Eosinophill percentage
0.0074	Bundle branch block
0.0071	Purpura and other hemorrhagic conditions
0.0070	Cardiac conduction disorders
0.0070	D69 Purpura and other haemorrhagic conditions

NNM-Sparse-FW

Top Factor: 96 (Contribution: 0.1300)

0.0249	Ankle spacing width (right)
0.0187	Impedance of leg (left)
0.0154	proton pump inhibitor\|PPI
0.0153	Angina pectoris
0.0143	Whole body fat-free mass
0.0134	Non-cancer illness code, self-reported
0.0127	benzodiazepine\|sedative\|anxiety
0.0115	Ischemic Heart Disease
0.0111	Sitting height
0.0088	Leg predicted mass (left)
0.0088	Seated height
0.0085	Leg fat mass (left)
0.0084	Peak expiratory flow (PEF)
0.0072	Arm predicted mass (right)
0.0070	Age at first live birth

Raw Data

Top Factor: 61 (Contribution: 0.0849)

0.0324	Heel bone mineral density (BMD)
0.0322	Heel bone mineral density (BMD) T-score, automated
0.0322	Heel quantitative ultrasound index (QUI), direct entry
0.0258	Heel Broadband ultrasound attenuation, direct entry
0.0139	Urate
0.0119	Heel bone mineral density (BMD) T-score, automated (left)
0.0119	Heel quantitative ultrasound index (QUI), direct entry (left)
0.0119	Heel broadband ultrasound attenuation (left)
0.0116	Heel bone mineral density (BMD) (left)
0.0115	Heel bone mineral density (BMD) T-score, automated (right)
0.0115	Heel quantitative ultrasound index (QUI), direct entry (right)
0.0115	Heel broadband ultrasound attenuation (right)
0.0114	Heel bone mineral density (BMD) (right)
0.0103	Cerebrovascular disease
0.0102	Creatinine