Elsevier

Genomics

Volume 103, Issue 1, January 2014, Pages 56-64
Genomics

Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK)

https://doi.org/10.1016/j.ygeno.2013.12.005Get rights and content
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Highlights

  • We performed 20 Caucasian and Han Chinese whole-transcriptome sequencing.

  • Within-population novel splice variants are common.

  • Inter-population novel splice variants are rare.

  • We identified hnRNPK, among 23 genes that exhibit differential splicing.

Abstract

Gene expression variations (GEV) among different ethnic groups have been a subject matter for extensive study. Relatively less known is the extent of alternative splicing variations (ASV) in the context of ethnicity. We conducted a transcriptome sequencing study of 20 lymphoblastoid cell lines obtained from Caucasian and Han Chinese, and identified known genes that exhibit differential isoform abundance between the two ethnic groups. Among them hnRNPK, a co-factor of p53 (TP53), could be further replicated in a 39-sample cohort with TaqMan assay. Although within-population novel splice variants are common, inter-population novel splice variants are rare. We further analyzed 5.63 billion sequencing reads retrieved from the NCBI Sequence Read Archive and identified potential ethnic-specific transcribed regions.

Abbreviations

GEV
gene expression variation
ASV
alternative splicing variation
LCL
lymphoblastoid cell lines
CHB
Han Beijing Chinese
CEU
European sampled in Utah with ancestry from northern and western Europe
JPT
Japanese in Tokyo, Japan
YRI
Yoruba in Ibadan, Nigeria
SRA
NCBI Sequence Read Archive
TR
Transcribed Region
nTR
novel Transcribed Region
HC
High Confidence
LS
Loose Set

Keywords

Ethnicity
Splicing variation
Transcriptomics
High-throughput sequencing

Cited by (0)

1

Present address of Keng-Po Lai: School of Biological Sciences, The University of Hong Kong, Hong Kong.