title: Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK).
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.
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong. Electronic address: marcowanger@gmail.com.
authors.forename: Jing-Woei
authors.initials: JW
authors.lastname: Li
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong. Electronic address: balllai@hku.hk.
authors.forename: Keng-Po
authors.initials: KP
authors.lastname: Lai
authors.affiliation: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong. Electronic address: akkching@gmail.com.
authors.forename: Arthur K K
authors.initials: AK
authors.lastname: Ching
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong. Electronic address: tf.chan@cuhk.edu.hk.
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
mesh_terms: D017398:Alternative Splicing; D044466:Asian People / Q000235:genetics*; D002478:Cells, Cultured; D002874:Chromosome Mapping; D014644:Genetic Variation; D015894:Genome, Human; D034641:Heterogeneous-Nuclear Ribonucleoprotein K / Q000235:genetics*; D006801:Humans; D015201:Meta-Analysis as Topic; D020033:Protein Isoforms / Q000235:genetics; D012261:Ribonucleoproteins / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D044465:White People / Q000235:genetics*
chemical_list: D034641:Heterogeneous-Nuclear Ribonucleoprotein K; D020033:Protein Isoforms; D012261:Ribonucleoproteins; C072074:HNRNPK protein, human
keywords: Ethnicity; High-throughput sequencing; Splicing variation; Transcriptomics