Whole genome sequencing data for two individuals of Pakistani descent

被引：0

作者：

Shahid Y. Khan

Firoz Kabir

Oussama M’Hamdi

Xiaodong Jiao

Muhammad Asif Naeem

Shaheen N. Khan

Sheikh Riazuddin

J. Fielding Hejtmancik

S. Amer Riazuddin

机构：

[1] The Wilmer Eye Institute,

[2] Johns Hopkins University School of Medicine,undefined

[3] Ophthalmic Genetics and Visual Function Branch,undefined

[4] National Eye Institute,undefined

[5] National Institutes of Health,undefined

[6] National Centre of Excellence in Molecular Biology,undefined

[7] University of the Punjab,undefined

来源：

Scientific Data | / 5卷

关键词：

D O I：

暂无

中图分类号：

学科分类号：

摘要：

Here we report next-generation based whole genome sequencing of two individuals (H1 and H2) from a family of Pakistani descent. The genomic DNA was used to prepare paired-end libraries for whole-genome sequencing. Deep sequencing yielded 706.49 and 778.12 million mapped reads corresponding to 70.64 and 77.81 Gb sequence data and 23× and 25× average coverage for H1 and H2, respectively. Notably, a total of 448,544 and 470,683 novel variants, not present in the single nucleotide polymorphism database (dbSNP), were identified in H1 and H2, respectively. Comparative analysis identified 2,415,852 variants common in both genomes including 240,181 variants absent in the dbSNP. Principal component analysis linked the ancestry of both genomes with South Asian populations. In conclusion, we report whole genome sequences of two individuals from a family of Pakistani descent.

引用

共 50 条

[21] Identifying the genetic causes of phenotypically diagnosed Pakistani mucopolysaccharidoses patients by whole genome sequencing [J].

Gul, Rutaba ;

Firasat, Sabika ;

Schubert, Mikkel ;

Ullah, Asmat ;

Pena, Elionora ;

Thuesen, Anne C. B. ;

Hussain, Mulazim ;

Staeger, Frederik F. ;

Gjesing, Anette P. ;

Albrechtsen, Anders ;

Hansen, Torben .

FRONTIERS IN GENETICS, 2023, 14

[22] A novel strategy for clustering major depression individuals using whole-genome sequencing variant data [J].

Chenglong Yu ;

Bernhard T. Baune ;

Julio Licinio ;

Ma-Li Wong .

Scientific Reports, 7

[23] Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis [J].

Savage, Abigail L. ;

Iacoangeli, Alfredo ;

Schumann, Gerald G. ;

Rubio-Roldan, Alejandro ;

Garcia-Perez, Jose L. ;

Al Khleifat, Ahmad ;

Koks, Sulev ;

Bubb, Vivien J. ;

Al-Chalabi, Ammar ;

Quinn, John P. .

GENE, 2022, 843

[24] Data of whole genome sequencing of five garden asparagus (Asparagus officinalis) individuals with the MinION nanopore sequencer [J].

Tsugama, Daisuke ;

Fujino, Kaien .

DATA IN BRIEF, 2020, 28

[25] A novel strategy for clustering major depression individuals using whole-genome sequencing variant data [J].

Yu, Chenglong ;

Baune, Bernhard T. ;

Licinio, Julio ;

Wong, Ma-Li .

SCIENTIFIC REPORTS, 2017, 7

[26] Chromosome genome assembly and whole genome sequencing of 110 individuals of Conogethes punctiferalis (Guenee) [J].

Gao, Bojia ;

Peng, Yan ;

Jin, Minghui ;

Zhang, Lei ;

Han, Xiu ;

Wu, Chao ;

Yuan, He ;

Awawing, Andongma ;

Zheng, Fangqiang ;

Li, Xiangdong ;

Xiao, Yutao .

SCIENTIFIC DATA, 2023, 10 (01)

[27] Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data [J].

Johnson, Kelsey E. ;

Adams, Christopher J. ;

Voight, Benjamin F. .

METHODS IN ECOLOGY AND EVOLUTION, 2022, 13 (11) :2429-2442

[28] A systems biology analysis for the whole genome sequencing data [J].

Jhamb, Deepali ;

Pradhan, Meeta P. ;

Desai, Akshay ;

Palakal, Mathew J. ;

Duraiswamy, Premkumar .

2014 IEEE 4TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS), 2014,

[29] Typing methods based on whole genome sequencing data [J].

Uelze, Laura ;

Gruetzke, Josephine ;

Borowiak, Maria ;

Hammerl, Jens Andre ;

Juraschek, Katharina ;

Deneke, Carlus ;

Tausch, Simon H. ;

Malorny, Burkhard .

ONE HEALTH OUTLOOK, 2020, 2 (01)

[30] Typing methods based on whole genome sequencing data [J].

Laura Uelze ;

Josephine Grützke ;

Maria Borowiak ;

Jens Andre Hammerl ;

Katharina Juraschek ;

Carlus Deneke ;

Simon H. Tausch ;

Burkhard Malorny .

One Health Outlook, 2

← 1 2 3 4 5 →