INDEX-db: The Indian Exome Reference Database (Phase I)

被引：28

作者：

Ahmed, Husayn P. ^{[1
,2
]}

Vidhya, V. ^{[3
]}

More, Ravi Prabhakar ^{[1
]}

Viswanath, Biju ^{[4
,5
]}

Jain, Sanjeev ^{[4
,5
]}

Rao, Mahendra S. ^{[3
,6
]}

Mukherjee, Odity ^{[3
,6
]}

Rao, Naren P. ^{[5
]}

Narayanaswamy, Janardhanan C. ^{[5
]}

Sivakumar, Palanimuthu T. ^{[5
]}

ArunKandaswamy ^{[5
]}

MuralidharanKesavan ^{[5
]}

Mehta, Urvakhsh-Meherwan ^{[5
]}

GanesanVenkatasubramanian ^{[5
]}

John, P. John ^{[5
]}

MeeraPurushottam

RamakrishnanKannan ^{[5
]}

Mehta, Bhupesh ^{[5
]}

ThennarasuKandavel ^{[5
]}

Binukumar, B. ^{[5
]}

JitenderSaini ^{[5
]}

Jayarajan, Deepak ^{[5
]}

Shyamsundar, A. ^{[5
]}

Moirangthem, Sydney ^{[5
]}

Kumar, Vijay G. ^{[5
]}

JagadishaThirthalli ^{[5
]}

Chandra, Prabha S. ^{[5
]}

Gangadhar, Bangalore N. ^{[5
]}

Murthy, Pratima ^{[5
]}

Panicker, Mitradas M.

Bhalla, Upinder S. ^{[7
]}

SumantraChattarji ^{[6
,7
]}

VivekBenegal ^{[5
]}

Varghese, Mathew ^{[5
]}

Reddy, Janardhan Y. C. ^{[5
]}

Raghu, Padinjat ^{[7
]}

机构：

[1] TIFR, NCBS, Accelerator Program Discovery Brain Disorders Usi, Bengaluru, India

[2] IBAB, Bengaluru, India

[3] Inst Stem Cell Biol & Regenerat Med InStem, CBDR, Accelerator Program Discovery Brain Disorders Usi, Bellary Rd, Bengaluru 560065, India

[4] NIMHANS, Dept Psychiat, Bengaluru, India

[5] NIMHANS, Bengaluru, India

[6] Inst Stem Cell Biol & Regenerat Med InStem, Bengaluru, India

[7] TIFR, NCB, Bengaluru, India

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 2019年 / 26卷 / 03期

关键词：

genetic variations catalogue; Indian population; population-specific database; whole exome sequencing; COPY-NUMBER VARIATIONS; GENETIC-VARIATION; QUALITY-CONTROL; DISCOVERY; MUTATION; IMPACT; CANCER;

D O I：

10.1089/cmb.2018.0199

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.

引用

页码：225 / 234

页数：10

共 46 条

[41] Extremely low-coverage whole genome sequencing in South Asians captures population genomics information [J].

Rustagi, Navin ;

Zhou, Anbo ;

Watkins, W. Scott ;

Gedvilaite, Erika ;

Wang, Shuoguo ;

Ramesh, Naveen ;

Muzny, Donna ;

Gibbs, Richard A. ;

Jorde, Lynn B. ;

Yu, Fuli ;

Xing, Jinchuan .

BMC GENOMICS, 2017, 18

[42] Quality control and preprocessing of metagenomic datasets [J].

Schmieder, Robert ;

Edwards, Robert .

BIOINFORMATICS, 2011, 27 (06) :863-864

[43] The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives [J].

Simons, Yuval B. ;

Sella, Guy .

CURRENT OPINION IN GENETICS & DEVELOPMENT, 2016, 41 :150-158

[44] JBrowse: A next-generation genome browser [J].

Skinner, Mitchell E. ;

Uzilov, Andrew V. ;

Stein, Lincoln D. ;

Mungall, Christopher J. ;

Holmes, Ian H. .

GENOME RESEARCH, 2009, 19 (09) :1630-1638

[45] TMC-SNPdb: an Indian germline variant database derived from whole exome sequences [J].

Upadhyay, Pawan ;

Gardi, Nilesh ;

Desai, Sanket ;

Sahoo, Bikram ;

Singh, Ankita ;

Togar, Trupti ;

Iyer, Prajish ;

Prasad, Ratnam ;

Chandrani, Pratik ;

Gupta, Sudeep ;

Dutt, Amit .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2016,

[46] ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data [J].

Wang, Kai ;

Li, Mingyao ;

Hakonarson, Hakon .

NUCLEIC ACIDS RESEARCH, 2010, 38 (16) :e164

← 1 2 3 4 5 →