Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases.
Systemic Autoimmune Diseases, a group of chronic inflammatory conditions, have variable symptoms and difficult diagnosis. In order to reclassify them based on genetic markers rather than clinical criteria, we performed clustering of Single Nucleotide Polymorphisms. However naive approaches tend to g...
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doaj-7b1e72d9caf04eab9a1887589e435aff2020-11-25T01:30:57ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01118e016027010.1371/journal.pone.0160270Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases.Thomas CharlonManuel Martínez-BuenoLara Bossini-CastilloF David CarmonaAlessandro Di CaraJérôme WojcikSviatoslav VoloshynovskiyJavier MartínMarta E Alarcón-RiquelmeSystemic Autoimmune Diseases, a group of chronic inflammatory conditions, have variable symptoms and difficult diagnosis. In order to reclassify them based on genetic markers rather than clinical criteria, we performed clustering of Single Nucleotide Polymorphisms. However naive approaches tend to group patients primarily by their geographic origin. To reduce this "ancestry signal", we developed SNPClust, a method to select large sources of ancestry-independent genetic variations from all variations detected by Principal Component Analysis. Applied to a Systemic Lupus Erythematosus case control dataset, SNPClust successfully reduced the ancestry signal. Results were compared with association studies between the cases and controls without or with reference population stratification correction methods. SNPClust amplified the disease discriminating signal and the ratio of significant associations outside the HLA locus was greater compared to population stratification correction methods. SNPClust will enable the use of ancestry-independent genetic information in the reclassification of Systemic Autoimmune Diseases. SNPClust is available as an R package and demonstrated on the public Human Genome Diversity Project dataset at https://github.com/ThomasChln/snpclust.http://europepmc.org/articles/PMC4973908?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Thomas Charlon Manuel Martínez-Bueno Lara Bossini-Castillo F David Carmona Alessandro Di Cara Jérôme Wojcik Sviatoslav Voloshynovskiy Javier Martín Marta E Alarcón-Riquelme |
spellingShingle |
Thomas Charlon Manuel Martínez-Bueno Lara Bossini-Castillo F David Carmona Alessandro Di Cara Jérôme Wojcik Sviatoslav Voloshynovskiy Javier Martín Marta E Alarcón-Riquelme Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. PLoS ONE |
author_facet |
Thomas Charlon Manuel Martínez-Bueno Lara Bossini-Castillo F David Carmona Alessandro Di Cara Jérôme Wojcik Sviatoslav Voloshynovskiy Javier Martín Marta E Alarcón-Riquelme |
author_sort |
Thomas Charlon |
title |
Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. |
title_short |
Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. |
title_full |
Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. |
title_fullStr |
Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. |
title_full_unstemmed |
Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. |
title_sort |
single nucleotide polymorphism clustering in systemic autoimmune diseases. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2016-01-01 |
description |
Systemic Autoimmune Diseases, a group of chronic inflammatory conditions, have variable symptoms and difficult diagnosis. In order to reclassify them based on genetic markers rather than clinical criteria, we performed clustering of Single Nucleotide Polymorphisms. However naive approaches tend to group patients primarily by their geographic origin. To reduce this "ancestry signal", we developed SNPClust, a method to select large sources of ancestry-independent genetic variations from all variations detected by Principal Component Analysis. Applied to a Systemic Lupus Erythematosus case control dataset, SNPClust successfully reduced the ancestry signal. Results were compared with association studies between the cases and controls without or with reference population stratification correction methods. SNPClust amplified the disease discriminating signal and the ratio of significant associations outside the HLA locus was greater compared to population stratification correction methods. SNPClust will enable the use of ancestry-independent genetic information in the reclassification of Systemic Autoimmune Diseases. SNPClust is available as an R package and demonstrated on the public Human Genome Diversity Project dataset at https://github.com/ThomasChln/snpclust. |
url |
http://europepmc.org/articles/PMC4973908?pdf=render |
work_keys_str_mv |
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