STAMPEED: Whole Genome Association Analysis of Hematopoietic Cell Transplant (HCT) Outcomes

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Ancestry (1)

race.mcd - Minimum covariance determinant defined genetic analysis group for all samples (phv00428429.v1.p1)

Demographics (4)

d.age - Donor age (phv00428451.v1.p1)
p.age - Recipient age (phv00428450.v1.p1)
sex - Genetic sex coded as M=male and F=female (phv00428425.v1.p1)
yeartx - Year of transplant (phv00428462.v1.p1)

Race and Ethnicity (1)

race.s - Self-identified race (phv00428430.v1.p1)

Other (70)

ant.excl - TRUE for samples that received active drug in clinical trials and recommend exclusion from analysis of delant endpoint (antigenemia) (phv00493898.v1.p1)
cohort - Cohort sample was genotyped in: cohort 1 (c1) or cohort 2 (2a, 2b, 2c) (phv00428453.v1.p1)
comment.kary - Primarily identifying chromosomal anomaly (phv00428428.v1.p1)
CONSENT - Consent group as determined by FHCRC IRB (phv00428421.v1.p1)
dayant - For delant==0 last observed time before which no event had occurred or until a competing risk occurred. For delant==1 time until event had occurred. (phv00493897.v1.p1)
daycgvh - Days until chronic GVHD or until censoring or a competing risk event (phv00493912.v1.p1)
daycmv - For delcmv==0 last observed time before which no event had occurred or until a competing risk occurred. For delcmv==1 time until event had occurred. (phv00493900.v1.p1)
daygut2 - Days until acute GVHD stage 2-4 or until censoring or a competing risk event (phv00493910.v1.p1)
daygvh2 - Days until acute GVHD grade 2-4 or until censoring or a competing risk event (phv00493904.v1.p1)
daygvh2b - Days until acute GVHD grade 2b-4 or until censoring or a competing risk event (phv00493906.v1.p1)
daygvh3 - Days until acute GVHD grade 3-4 or until censoring or a competing risk event (phv00493908.v1.p1)
daynrm - Days survived without relapse or until censoring or a competing risk event (phv00428471.v1.p1)
dayrel - Days until relapse or until censoring or a competing risk event (phv00493914.v1.p1)
dayrrm - Days survived until relapse related event or until censoring or a competing risk event (phv00428473.v1.p1)
daysur - Days survived or until censoring or a competing risk event (phv00428475.v1.p1)
delant - Any antigenemia (ANT/AG), PCR positive cases vs no. Competing risk of death set to 0. (phv00493896.v1.p1)
delcgvh - Chronic GVHD. One means event and zero means censored or competing risk event. (phv00493911.v1.p1)
delcmv - Any CMV disease (virus in an organ with symptoms) vs no disease. Competing risk of death set to 0. (phv00493899.v1.p1)
delgut2 - Acute GVHD gut stage 2-4. One means event and zero means censored or competing risk event. (phv00493909.v1.p1)
delgvh2 - Acute GVHD grade 2-4. One means event and zero means censored or competing risk event. (phv00493903.v1.p1)
delgvh2b - Acute GVHD grade 2b-4. One means event and zero means censored or competing risk event. (phv00493905.v1.p1)
delgvh3 - Acute GVHD grade 3-4. One means event and zero means censored or competing risk event. (phv00493907.v1.p1)
delnrm - Non-relapse mortality (NRM). One means event and zero means censored or competing risk event. (phv00428470.v1.p1)
delrel - Relapse. One means event and zero means censored or competing risk event. (phv00493913.v1.p1)
delrrm - Relapse mortality (RRM). One means event and zero means censored or competing risk event. (phv00428472.v1.p1)
delsur - Overall survival (OS). One means event and zero means censored or competing risk event. (phv00428474.v1.p1)
dna.source - Source of DNA, either cell line (B-LCL) or blood (Native) (phv00428455.v1.p1)
dnrExpRel - Computed donor recipient relationship from PC-Relate - Deg2 (second-degree relative), Deg2 (third-degree relative), FS (full sibling), Other (relative of unknown relationship), PO (parent offspring), U (unrelated) (phv00428464.v1.p1)
dnrRel - Annotated donor recipient relationship from transplant records confirmed by PC-Relate genetic calculations (phv00428465.v1.p1)
doncmv - Donor sero-postive (+) or sero-negative (-) for CMV (phv00493902.v1.p1)
double.donor - TRUE to identify donors who donated to more than one recipient (phv00428424.v1.p1)
dxgroup - Recipient disease type - ALL (acute lymphoblastic leukemia), ANL (acute non-lymphoblastic leukemia, primarily acute myeloid leukemia), CLL (chronic lymphocytic leukemia), CML (chronic myeloid leukemia), HD (hodgkin disease), MDS (myelodysplastic syndromes), MM (multiple myeloma), NHL (non-hodgkin's lymphoma) (phv00428458.v1.p1)
filter.X - Whether to filter the X chromosome due to abnormal karyotype (phv00428427.v1.p1)
ftom - Female donor to male recipient (phv00428457.v1.p1)
HLA_A_Allele1 - Historical typing for HLA-A alleles informed by HIBAG imputed HLA-A alleles (phv00428432.v1.p1)
HLA_A_Allele2 - Historical typing for HLA-A alleles informed by HIBAG imputed HLA-A alleles (phv00428433.v1.p1)
HLA_B_Allele1 - Historical typing for HLA-B alleles informed by HIBAG imputed HLA-B alleles (phv00428434.v1.p1)
HLA_B_Allele2 - Historical typing for HLA-B alleles informed by HIBAG imputed HLA-B alleles (phv00428435.v1.p1)
HLA_C_Allele1 - Historical typing for HLA-C alleles informed by HIBAG imputed HLA-C alleles (phv00428436.v1.p1)
HLA_C_Allele2 - Historical typing for HLA-C alleles informed by HIBAG imputed HLA-C alleles (phv00428437.v1.p1)
HLA_DPA1_Allele1 - NGS DPA1 typing for mostly cohort 1 samples and historical typing for mostly cohort 2 samples informed by HIBAG imputed DPA1 alleles (phv00428446.v1.p1)
HLA_DPA1_Allele2 - NGS DPA1 typing for mostly cohort 1 samples and historical typing for mostly cohort 2 samples informed by HIBAG imputed DPA1 alleles (phv00428447.v1.p1)
HLA_DPB1_Allele1 - NGS DPB1 typing for mostly cohort 1 samples and historical typing for mostly cohort 2 samples informed by HIBAG imputed DPB1 alleles (phv00428444.v1.p1)
HLA_DPB1_Allele2 - NGS DPB1 typing for mostly cohort 1 samples and historical typing for mostly cohort 2 samples informed by HIBAG imputed DPB1 alleles (phv00428445.v1.p1)
HLA_DQA1_Allele1 - NGS DQA1 typing for mostly cohort 1 samples and historical typing for mostly cohort 2 samples informed by HIBAG imputed DQA1 alleles (phv00428442.v1.p1)
HLA_DQA1_Allele2 - NGS DQA1 typing for mostly cohort 1 samples and historical typing for mostly cohort 2 samples informed by HIBAG imputed DQA1 alleles (phv00428443.v1.p1)
HLA_DQB1_Allele1 - Historical typing for HLA-DQB1 alleles informed by HIBAG imputed HLA-DQB1 alleles (phv00428440.v1.p1)
HLA_DQB1_Allele2 - Historical typing for HLA-DQB1 alleles informed by HIBAG imputed HLA-DQB1 alleles (phv00428441.v1.p1)
HLA_DRB1_Allele1 - Historical typing for HLA-DRB1 alleles informed by HIBAG imputed HLA-DRB1 alleles (phv00428438.v1.p1)
HLA_DRB1_Allele2 - Historical typing for HLA-DRB1 alleles informed by HIBAG imputed HLA-DRB1 alleles (phv00428439.v1.p1)
inclgvh2 - This variable is 1 for patients who did NOT receive Anti-thymocyte globulin (ATG) and post-treatment cytoxan and 0 otherwise. (phv00493915.v1.p1)
karyotype - Sex chromosome karyotype if abnormal (phv00428426.v1.p1)
kc - Kinship coefficient between recipient and donor when genotypes for both were available calculated using PC-Relate (phv00428463.v1.p1)
missing.e2.auto - Fraction of autosomal genotype calls missing over all autosomal snps with missing.n1 < 0.05 (phv00428454.v1.p1)
n.10.match - Number of HLA-A, B, C, DRB1, DQB1 alleles that match between recipient and donor (phv00428466.v1.p1)
n.16.match - Number of HLA-A, B, C, DRB1, DQB1, DQA1, DPB1, DPA1 alleles that match between recipient and donor (phv00428467.v1.p1)
pairID - Identifier for each recipient/donor pair where both samples have genotype data. Missing for singletons. (phv00428449.v1.p1)
patcmv - Recipient sero-postive (+) or sero-negative (-) for CMV (phv00493901.v1.p1)
pbsc - One for peripheral blood stem cell (pbsc) donor (phv00428456.v1.p1)
plate - Genotyping plate (phv00428452.v1.p1)
preptype - MyeloAblative (MA) and Non-MyeloAblative (NMA) conditioning prior to transplant (phv00428461.v1.p1)
riskgrp - General classification of risk of relapse/mortality after transplant. The ordering of the categories 1-3 equals low-high risk. (phv00428459.v1.p1)
SAMPLE_ID - Unique identifier for each sample (phv00428448.v1.p1)
SAMPLE_ID - Sample ID (phv00428423.v1.p1)
SUBJECT_ID - Subject ID (phv00428469.v1.p1)
SUBJECT_ID - Subject ID (phv00428431.v1.p1)
SUBJECT_ID - Subject ID (phv00428420.v1.p1)
SUBJECT_ID - Subject ID (phv00428422.v1.p1)
tbi900 - Dose of TBI during conditioning was >= 900 cGy (phv00428460.v1.p1)
tpID - Transplant identifier (phv00428468.v1.p1)