Whole genome genotyping technologies on the BeadArray platform.

Biotechnol J. 2007 Jan;2(1):41-9

Authors: Steemers FJ, Gunderson KL

The ability to simultaneously genotype hundreds of thousands of single-nucleotide polymorphisms (SNPs) in a single assay has recently become feasible due to innovative combinations of assay and array platform multiplexing. In this review, we describe the development of the Infinium whole genome genotyping technology and the BeadArray platform. We discuss the automated use and performance of a series of genotyping BeadChips, including data quality, technology scalability, and flexibility in designing array content. We describe high-density tag SNP-based Bead-Chips and various multi-sample BeadChip configurations with their respective applications. These technologies are enabling large-scale whole genome association studies that have the potential to revolutionize our ability to detect common genetic variants with a significant role in identifying disease-associated loci, proteins, biomarkers, and pharmacogenomic responses.

PMID: 17225249 [PubMed - indexed for MEDLINE]

Leveraging the HapMap correlation structure in association studies.

Am J Hum Genet. 2007 Apr;80(4):683-91

Authors: Zaitlen N, Kang HM, Eskin E, Halperin E

Recent high-throughput genotyping technologies, such as the Affymetrix 500k array and the Illumina HumanHap 550 beadchip, have driven down the costs of association studies and have enabled the measurement of single-nucleotide polymorphism (SNP) allele frequency differences between case and control populations on a genomewide scale. A key aspect in the efficiency of association studies is the notion of "indirect association," where only a subset of SNPs are collected to serve as proxies for the uncollected SNPs, taking advantage of the correlation structure between SNPs. Recently, a new class of methods for indirect association, multimarker methods, has been proposed. Although the multimarker methods are a considerable advancement, current methods do not fully take advantage of the correlation structure between SNPs and their multimarker proxies. In this article, we propose a novel multimarker indirect-association method, WHAP, that is based on a weighted sum of the haplotype frequency differences. In contrast to traditional indirect-association methods, we show analytically that there is a considerable gain in power achieved by our method compared with both single-marker and multimarker tests, as well as traditional haplotype-based tests. Our results are supported by empirical evaluation across the HapMap reference panel data sets, and a software implementation for the Affymetrix 500k and Illumina HumanHap 550 chips is available for download.

PMID: 17357074 [PubMed - indexed for MEDLINE]

Atypical teratoid/rhabdoid tumor in a patient with Beckwith-Wiedemann syndrome.

Am J Med Genet A. 2007 Aug 1;143A(15):1767-70

Authors: Jackson EM, Shaikh TH, Zhang F, Wainwright LM, Storm PB, Hakonarson H, Zackai EH, Biegel JA

Beckwith-Wiedemann syndrome (BWS) is a genetic disorder associated with an increased risk of childhood tumors. Here we describe a patient with BWS who developed a central nervous system atypical teratoid/rhabdoid tumor (AT/RT). To our knowledge, despite the known cancer predisposition, this patient is the first described with BWS to develop an AT/RT. Due to the high propensity of these patients to develop childhood tumors, in addition to routine diagnostic tests, analysis of the tumor DNA using the Illumina Infinium whole-genome genotyping 550K Beadchip was performed to investigate a possible common underlying mechanism for his BWS and AT/RT. The only alteration detected was monosomy 22, which was accompanied by a somatic mutation in the INI1 rhabdoid tumor gene. These results suggest that, despite an underlying cancer predisposition, the occurrence of BWS and AT/RT in this patient may be unrelated.

PMID: 17603804 [PubMed - indexed for MEDLINE]

Identification of two novel DQA1 alleles, DQA1*0107 and DQA1*0602, by sequence-based typing in the GoKinD population.

Hum Immunol. 2005 Dec;66(12):1248-53

Authors: Hancock LN, Cordovado SK, Hendrix M, Simone AE, Mueller PW

Two novel DQA1 alleles, DQA1*0107 and DQA1*0602, were discovered using DQA1 sequence-based typing (SBT) in participants in the Genetics of Kidneys in Diabetes (GoKinD) Study. The DQA1*0107 allele, found in three unrelated Caucasian participants, contains a novel polymorphism at codon 79 of exon 2 (CGC-->TGC), which results in an amino acid change from an arginine to a cysteine. The participants containing this novel polymorphism also had a 1-bp insertion in intron 2 that is common to the *01 alleles. The DQA1*0602 allele, found in one Caucasian participant, contains a novel polymorphism at codon 139 of exon 3 (AGC-->CGC), which results in an amino acid change from a serine to an arginine. Additionally, the *0602 allele has a base change in intron 1 that is common to the *06 alleles. Both new alleles were isolated using single-allele amplification SBT and confirmed using sequence-specific primer amplification.

PMID: 16690412 [PubMed - indexed for MEDLINE]