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Imputation of KIR Types from SNP Variation Data

Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases... Full description

Journal Title: The American Journal of Human Genetics 01 October 2015, Vol.97(4), pp.593-607
Main Author: Vukcevic, Damjan
Other Authors: Traherne, James a , Næss, Sigrid , Ellinghaus, Eva , Kamatani, Yoichiro , Dilthey, Alexander , Lathrop, Mark , Karlsen, Tom h , Franke, Andre , Moffatt, Miriam , Cookson, William , Trowsdale, John , Mcvean, Gil , Sawcer, Stephen , Leslie, Stephen
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 0002-9297 ; E-ISSN: 1537-6605 ; DOI: 10.1016/j.ajhg.2015.09.005
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recordid: elsevier_sdoi_10_1016_j_ajhg_2015_09_005
title: Imputation of KIR Types from SNP Variation Data
format: Article
creator:
  • Vukcevic, Damjan
  • Traherne, James a
  • Næss, Sigrid
  • Ellinghaus, Eva
  • Kamatani, Yoichiro
  • Dilthey, Alexander
  • Lathrop, Mark
  • Karlsen, Tom h
  • Franke, Andre
  • Moffatt, Miriam
  • Cookson, William
  • Trowsdale, John
  • Mcvean, Gil
  • Sawcer, Stephen
  • Leslie, Stephen
subjects:
  • Biology
ispartof: The American Journal of Human Genetics, 01 October 2015, Vol.97(4), pp.593-607
description: Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed...
language: eng
source:
identifier: ISSN: 0002-9297 ; E-ISSN: 1537-6605 ; DOI: 10.1016/j.ajhg.2015.09.005
fulltext: fulltext
issn:
  • 0002-9297
  • 00029297
  • 1537-6605
  • 15376605
url: Link


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descriptionLarge population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed...
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Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed...

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Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed...

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