Han Chinese Cell and Genome Bank in Taiwan: Purpose, Design and Ethical Considerations

Pan, Wen Harn; Fann, Cathy S.J.; Wu, Jer Yuarn; Hung, Yung; Ho, Margaret S.; Tai, Terence Hua; Chen, Ying‐Ju; Liao, Chung Ju; Yang, Meng; Cheng, Andrew Tai Ann; Chen, Yuan Tsong

doi:10.1159/000091834

Cited by 88 publications

(89 citation statements)

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“…The control group (N = 2000, with nearly equal proportions of men and women) was randomly selected from the Han-Chinese Cell and Genome Bank in Taiwan reported previously. 20 In brief, more than 3300 healthy controls were recruited via a stratified, 3-staged probability clustering sampling scheme through the registry of all the 329 nonaboriginal townships or city districts in Taiwan. The study was approved by the institutional review board of all the participating hospitals and Academia Sinica, Taiwan and written informed consent were obtained from all of the participants.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association study of bipolar I disorder in the Han Chinese population

et al. 2010

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We report the first genome-wide association study in 1000 bipolar I patients and 1000 controls, with a replication of the top hits in another 409 cases and 1000 controls in the Han Chinese population. Four regions with most strongly associated single-nucleotide polymorphisms (SNPs) were detected, of which three were not found in previous GWA studies in the Caucasian populations. Among them, SNPs close to specificity protein 8 (SP8) and ST8 a-Nacetyl-neuraminide a-2,8-sialyltransferase (ST8SIA2) are associated with Bipolar I, with Pvalues of 4.87 Â 10 À7 (rs2709736) and 6.05 Â 10 À6 (rs8040009), respectively. We have also identified SNPs in potassium channel tetramerization domain containing 12 gene (KCTD12) (rs2073831, P = 9.74 Â 10 À6 ) and in CACNB2 (Calcium channel, voltage-dependent, b-2 subunit) gene (rs11013860, P = 5.15 Â 10 À5 ), One SNP nearby the rs1938526 SNP of ANK3 gene and another SNP nearby the SNP rs11720452 in chromosome 3 reported in previous GWA studies also showed suggestive association in this study (P = 6.55 Â 10 À5 and P = 1.48 Â 10 À5 , respectively). This may suggest that there are common and population-specific susceptibility genes for bipolar I disorder.

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Section: Methodsmentioning

confidence: 99%

Genome-wide association study of bipolar I disorder in the Han Chinese population

et al. 2010

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“…We calculated quality indices and established their empirical distributions based on SNP array data from the Taiwan Han Chinese Cell and Genome Bank [52] and the International HapMap Project [13-16]. Values of quality indices were fitted by lognormal distributions and examined by Kolmogorov-Smirnov goodness-of-fit tests [55].…”

Section: Resultsmentioning

confidence: 99%

“…Samples 1 - 4 were individual DNA with good quality from the Taiwan Han Chinese Cell and Genome Bank [52] and genotyped using arrays beyond expiration date (expired arrays); Samples 5 - 8 were pooled DNA of multiple individuals from the Taiwan Young-Onset Hypertension Study [5] and genotyped using arrays prior to expiration date (unexpired arrays). All the eight samples were genotyped with the Affymetrix Human Mapping 500K Set (Nsp and Sty arrays), and the quality index Q 2 was calculated for the Nsp array and Sty array and the "Merge" array which contains all SNPs on the Nsp array and Sty array.…”

Section: Resultsmentioning

confidence: 99%

“…The performance of Samples 5 - 8 was worse than that of Samples 1 - 4. The same analysis method was applied to 448 unselected individuals, which were recruited by the Taiwan Han Chinese Cell and Genome Bank [52] and genotyped using unexpired arrays. The majority of the samples had low quality indices for both SNP arrays and was categorized as "good quality"; four representative samples (Samples 9 - 12) were shown in Figure 2 for illustration.…”

Section: Resultsmentioning

confidence: 99%

“…Samples used in our analyses were from three genomic projects, the Taiwan Han Chinese Cell and Genome Bank [52], the International HapMap Project [13-16], and the Taiwan Young-Onset Hypertension Study [5]. The first project provides 367 and 448 Han Chinese samples from the Taiwan (TWN) population genotyped using the Affymetrix Human Mapping 100K Set and 500K Set, respectively.…”

Section: Methodsmentioning

confidence: 99%

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SAQC: SNP Array Quality Control

et al. 2011

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BackgroundGenome-wide single-nucleotide polymorphism (SNP) arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed.ResultsWe developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs) from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples.ConclusionsThis study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC). SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm).

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Overlapping High-Resolution Copy Number Alterations in Cancer Genomes Identified Putative Cancer Genes in Hepatocellular Carcinoma

et al. 2010

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Recurrent cancer genome aberrations are indicators of residing crucial cancer genes. Although recent advances in genomic technologies have led to a global view of cancer genome aberrations, the identification of target genes and biomarkers from the aberrant loci remains difficult. To facilitate searches of cancer genes in human hepatocellular carcinoma (HCC), we established a comprehensive protocol to analyze copy number alterations (CNAs) in cancer genomes using high-density single nucleotide polymorphism arrays with unpaired reference genomes. We identified common HCC genes by overlapping the shared aberrant loci in multiple cell lines with functional validation and clinical implications. A total of 653 amplicons and 57 homozygous deletions (HDs) were revealed in 23 cell lines. To search for novel HCC genes, we overlapped aberrant loci to uncover 6 HDs and 126 amplicons shared by at least two cell lines. We selected two novel genes, fibronectin type III domain containing 3B (FNDC3B) at the 3q26.3 overlapped amplicon and solute carrier family 29 member 2 (SLC29A2) at the 11q13.2 overlapped amplicon, to investigate their aberrations in HCC tumorigenesis. Aberrant up-regulation of FNDC3B and SLC29A2 occurred in multiple HCC data sets. Knockdown of these genes in amplified cells decreased cell proliferation, anchorage-independent growth, and tumor formation in xenograft models. Importantly, up-regulation of SLC29A2 in HCC tissues was significantly associated with advanced stages (P 5 0.0031), vascular invasion (P 5 0.0353), and poor patient survival (P 5 0.0325). Overexpression of FNDC3B or SLC29A2 in unamplified HCC cells promoted cell proliferation through activation of the signal transducer and activator of transcription 3 signaling pathway. Conclusion: A standardized genome-wide CNA analysis protocol using data from user-generated or public domains normalized with unpaired reference genomes has been established to facilitate high-throughput detection of cancer genes as significant target genes and biomarkers for cancer diagnosis and therapy. (HEPATOLOGY 2010;52:1690-1701 Abbreviations: ADAM15, a disintegrin and metallopeptidase 15; AKT, v-akt murine thymoma viral oncogene homolog 1; AMACR, alpha-methylacyl-coenzyme A racemase; BCAS1, breast carcinoma amplified sequence 1; BRMS1, breast cancer metastasis suppressor 1; CCND1, cyclin D1; CDKN2A, cyclin-dependent kinase inhibitor 2A; CHN2, chimerin 2; CKS1B, CDC28 protein kinase regulatory subunit 1B; CNA, copy number alteration; DAB2, disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila); EBV, Epstein-Barr virus; EGFR, epidermal growth factor receptor; ETV1, ets variant 1; EVI1, ecotropic viral integration site 1; FNDC3B, fibronectin type III domain containing 3B; HCC, hepatocellular carcinoma; HD, homozygous deletion; ICN, inferred copy number; IHC, immunohistochemistry; LRP1B, low-density lipoprotein receptor-related protein 1B; LRP5, low-density lipoprotein receptor-related protein 5; Luc, luciferase; MAGI2, membrane associated guanylate kinase, W...

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Han Chinese Cell and Genome Bank in Taiwan: Purpose, Design and Ethical Considerations

Cited by 88 publications

References 3 publications

Genome-wide association study of bipolar I disorder in the Han Chinese population

Genome-wide association study of bipolar I disorder in the Han Chinese population

SAQC: SNP Array Quality Control

Overlapping High-Resolution Copy Number Alterations in Cancer Genomes Identified Putative Cancer Genes in Hepatocellular Carcinoma

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