PMID- 28532386
OWN - NLM
STAT- MEDLINE
DCOM- 20180108
LR  - 20221207
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 18
IP  - 1
DP  - 2017 May 22
TI  - Extremely low-coverage whole genome sequencing in South Asians captures 
      population genomics information.
PG  - 396
LID - 10.1186/s12864-017-3767-6 [doi]
LID - 396
AB  - BACKGROUND: The cost of Whole Genome Sequencing (WGS) has decreased tremendously 
      in recent years due to advances in next-generation sequencing technologies. 
      Nevertheless, the cost of carrying out large-scale cohort studies using WGS is 
      still daunting. Past simulation studies with coverage at ~2x have shown promise 
      for using low coverage WGS in studies focused on variant discovery, association 
      study replications, and population genomics characterization. However, the 
      performance of low coverage WGS in populations with a complex history and no 
      reference panel remains to be determined. RESULTS: South Indian populations are 
      known to have a complex population structure and are an example of a major 
      population group that lacks adequate reference panels. To test the performance of 
      extremely low-coverage WGS (EXL-WGS) in populations with a complex history and to 
      provide a reference resource for South Indian populations, we performed EXL-WGS 
      on 185 South Indian individuals from eight populations to ~1.6x coverage. Using 
      two variant discovery pipelines, SNPTools and GATK, we generated a consensus call 
      set that has ~90% sensitivity for identifying common variants (minor allele 
      frequency >/= 10%). Imputation further improves the sensitivity of our call set. In 
      addition, we obtained high-coverage for the whole mitochondrial genome to infer 
      the maternal lineage evolutionary history of the Indian samples. CONCLUSIONS: 
      Overall, we demonstrate that EXL-WGS with imputation can be a valuable study 
      design for variant discovery with a dramatically lower cost than standard WGS, 
      even in populations with a complex history and without available reference data. 
      In addition, the South Indian EXL-WGS data generated in this study will provide a 
      valuable resource for future Indian genomic studies.
FAU - Rustagi, Navin
AU  - Rustagi N
AD  - Department of Molecular and Human Genetics, Human Genome Sequencing Center, 
      Baylor College of Medicine, Houston, TX, 77030, USA.
FAU - Zhou, Anbo
AU  - Zhou A
AD  - Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The 
      State University of New Jersey, Piscataway, NJ, 08854, USA.
FAU - Watkins, W Scott
AU  - Watkins WS
AD  - Department of Human Genetics, Eccles Institute of Human Genetics, University of 
      Utah, Salt Lake City, UT, 84112, USA.
FAU - Gedvilaite, Erika
AU  - Gedvilaite E
AD  - Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The 
      State University of New Jersey, Piscataway, NJ, 08854, USA.
FAU - Wang, Shuoguo
AU  - Wang S
AD  - Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The 
      State University of New Jersey, Piscataway, NJ, 08854, USA.
FAU - Ramesh, Naveen
AU  - Ramesh N
AD  - Department of Molecular and Human Genetics, Human Genome Sequencing Center, 
      Baylor College of Medicine, Houston, TX, 77030, USA.
FAU - Muzny, Donna
AU  - Muzny D
AD  - Department of Molecular and Human Genetics, Human Genome Sequencing Center, 
      Baylor College of Medicine, Houston, TX, 77030, USA.
FAU - Gibbs, Richard A
AU  - Gibbs RA
AD  - Department of Molecular and Human Genetics, Human Genome Sequencing Center, 
      Baylor College of Medicine, Houston, TX, 77030, USA.
FAU - Jorde, Lynn B
AU  - Jorde LB
AD  - Department of Human Genetics, Eccles Institute of Human Genetics, University of 
      Utah, Salt Lake City, UT, 84112, USA. lbj@genetics.utah.edu.
FAU - Yu, Fuli
AU  - Yu F
AD  - Department of Molecular and Human Genetics, Human Genome Sequencing Center, 
      Baylor College of Medicine, Houston, TX, 77030, USA. fyu@bcm.edu.
FAU - Xing, Jinchuan
AU  - Xing J
AD  - Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The 
      State University of New Jersey, Piscataway, NJ, 08854, USA. 
      xing@biology.rutgers.edu.
LA  - eng
GR  - R00 HG005846/HG/NHGRI NIH HHS/United States
GR  - R01 GM059290/GM/NIGMS NIH HHS/United States
GR  - R35 GM118335/GM/NIGMS NIH HHS/United States
GR  - U54 HG003273/HG/NHGRI NIH HHS/United States
PT  - Journal Article
DEP - 20170522
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
SB  - IM
MH  - Asian People/*genetics
MH  - Genetic Variation
MH  - Genome, Mitochondrial/genetics
MH  - Humans
MH  - *Metagenomics
MH  - *Whole Genome Sequencing
PMC - PMC5440948
OTO - NOTNLM
OT  - Extremely low coverage
OT  - Imputation
OT  - Population structure
OT  - Single nucleotide variant
OT  - South Asian
OT  - Whole genome sequencing
EDAT- 2017/05/24 06:00
MHDA- 2018/01/09 06:00
PMCR- 2017/05/22
CRDT- 2017/05/24 06:00
PHST- 2016/09/14 00:00 [received]
PHST- 2017/05/07 00:00 [accepted]
PHST- 2017/05/24 06:00 [entrez]
PHST- 2017/05/24 06:00 [pubmed]
PHST- 2018/01/09 06:00 [medline]
PHST- 2017/05/22 00:00 [pmc-release]
AID - 10.1186/s12864-017-3767-6 [pii]
AID - 3767 [pii]
AID - 10.1186/s12864-017-3767-6 [doi]
PST - epublish
SO  - BMC Genomics. 2017 May 22;18(1):396. doi: 10.1186/s12864-017-3767-6.