Scopus
🔓 Açık Erişim YÖKSİS Eşleşti
Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage
Proceedings of the National Academy of Sciences of the United States of America · Haziran 2016
YÖKSİS Kayıtları
Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage
Proceedings of the National Academy of Sciences · 2016 SCI
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Makale Bilgileri
DergiProceedings of the National Academy of Sciences of the United States of America
Yayın TarihiHaziran 2016
Cilt / Sayfa113 · 6713-6718
Scopus ID2-s2.0-84974723289
Erişim🔓 Açık Erişim
Özet
Principal component analysis (PCA), homozygosity rate estimations, and linkage studiess in humans are classically conducted through genome-wide single-nucleotide variant arrays (GWSA). We compared whole-exome sequencing (WES) and GWSA for this purpose. We analyzed 110 subjects originating from different regions of the world, including North Africa and the Middle East, which are poorly covered by public databases and have high consanguinity rates. We tested and applied a number of quality control (QC) filters. Comparedwith GWSA, we found that WES provided an accurate prediction of population substructure using variants with a minor allele frequency > 2% (correlation = 0.89 with the PCA coordinates obtained by GWSA). WES also yielded highly reliable estimates of homozygosity rates using runs of homozygosity with a 1,000-kb window (correlation = 0.94 with the estimates provided by GWSA). Finally, homozygosity mapping analyses in 15 families including a single offspring with high homozygosity rates showed that WES provided 51% less genome- wide linkage information than GWSA overall but 97% more information for the coding regions. At the genome-wide scale, 76.3% of linked regions were found by both GWSA and WES, 17.7% were found by GWSA only, and 6.0% were found by WES only. For coding regions, the corresponding percentages were 83.5%, 7.4%, and 9.1%, respectively. With appropriate QC filters, WES can be used for PCA and adjustment for population substructure, estimating homozygosity rates in individuals, and powerful linkage analyses, particularly in coding regions.
Yazarlar (48)
1
Aziz Belkadi
2
Vincent Pedergnana
3
Aurélie Cobat
ORCID: 0000-0001-7209-6257
4
Yuval Itan
5
Quentin B. Vincent
6
Avinash Abhyankar
7
Lei Shang
8
Jamila El Baghdadi
9
Ahmed A. Bousfiha
10
Waleed Al-Herz
11
Cigdem Arikan
12
Peter Arkwright
13
Cigdem Aydogmus
14
Olivier Bernard
15
Lizbeth Blancas Galicia
16
Stéphanie Boisson-Dupuis
17
Damien Bonnet
18
Omar Boudghene Stambouli
19
Lobna Boussafara
20
Jeannette Boutros
21
Jacinta Bustamante
22
Michael J. Ciancanelli
23
Theresa Cole
24
Antonio Condino-Neto
ORCID: 0000-0002-1069-3117
25
Mukesh Desai
26
Claire Fieschi
27
José Luis Franco
28
Philippe Ichai
29
Emmanuelle Jouanguy
ORCID: 0000-0002-7358-9157
30
Melike Emiroglu
ORCID: 0000-0003-1307-0246
31
Sara S. Kilic
32
Seyed Alireza Mahdaviani
33
Nizar Malhaoui
34
Davood Mansouri
35
Nima Parvaneh
ORCID: 0000-0002-3397-9716
36
Capucine Picard
37
Anne Puel
38
Didier Raoult
39
Nima Rezaei
40
Ozden Sanal
41
Silvia Sanchez Ramon
42
François Vandenesch
43
Guillaume Vogt
44
Shen Ying Zhang
ORCID: 0000-0002-9449-3672
45
Alexandre Alcais
46
Bertrand Boisson
47
Jean Laurent Casanova
ORCID: 0000-0002-7782-4169
48
Laurent Abel
ORCID: 0000-0001-7016-6493
Anahtar Kelimeler
Exome sequencing
Genotyping array
Homozygosity mapping
Linkage analysis
Population structure
Kurumlar
Hassan II University of Casablanca
Casablanca Morocco
Hôpital Necker Enfants Malades
Paris France
Howard Hughes Medical Institute
Chevy Chase United States
l'Institut des Maladies Génétiques Imagine
Paris France
Military Hospital Mohammed V
Agdal Rabat Morocco
New York Genome Center
New York United States
Rockefeller University
New York United States
The Wellcome Centre for Human Genetics
Oxford United Kingdom
Metrikler
48
Atıf
48
Yazar
5
Anahtar Kelime