Pharmacogenomics: accessing important alleles by imputation from commercial genome-wide SNP arrays.

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Pharmacogenomics: accessing important alleles by imputation from commercial genome-wide SNP arrays.

Genet Mol Res. 2014;13(3):5713-21

Authors: Liboredo R, Pena SD

Abstract
Personalized medicine is becoming a medical reality, as important genotype-phenotype relationships are being unraveled. The availability of pharmacogenomic data is a key element of individualized care. In this study, we explored genotype imputation as a means to infer important pharmacogenomic alleles from a regular commercially available genome-wide SNP array. Using these arrays as a starting point can reduce testing costs, increasing access to these pharmacogenomic data and still retain a larger amount of genome-wide information. IMPUTE2 and MaCH-Admix were used to perform genotype imputation with a dense reference panel from 1000 Genomes data. We were able to correctly infer genotypes for the warfarin-related loci VKORC1 and CYP2C9 alleles *2, *3, *5, and *11 and also clopidogrel-related CYP2C19 alleles *2 and *17 for a small sample of Brazilian individuals, as well as for HapMap samples. The success of an imputation approach in admixed samples using publicly available reference panels can encourage further imputation initiatives in those populations.

PMID: 25117329 [PubMed - in process]

Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility.

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Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility.

Eur J Hum Genet. 2014 Aug 13;

Authors: Wang JC, Ross L, Mahon LW, Owen R, Hemmat M, Wang BT, El Naggar M, Kopita KA, Randolph LM, Chase JM, Matas Aguilera MJ, Siles JL, Church JA, Hauser N, Shen JJ, Jones MC, Wierenga KJ, Jiang Z, Haddadin M, Boyar FZ, Anguiano A, Strom CM, Sahoo T

Abstract
Copy neutral segments with allelic homozygosity, also known as regions of homozygosity (ROHs), are frequently identified in cases interrogated by oligonucleotide single-nucleotide polymorphism (oligo-SNP) microarrays. Presence of ROHs may be because of parental relatedness, chromosomal recombination or rearrangements and provides important clues regarding ancestral homozygosity, consanguinity or uniparental disomy. In this study of 14 574 consecutive cases, 832 (6%) were found to harbor one or more ROHs over 10 Mb, of which 651 cases (78%) had multiple ROHs, likely because of identity by descent (IBD), and 181 cases (22%) with ROHs involving a single chromosome. Parental relatedness was predicted to be first degree or closer in 5%, second in 9% and third in 19%. Of the 181 cases, 19 had ROHs for a whole chromosome revealing uniparental isodisomy (isoUPD). In all, 25 cases had significant ROHs involving a single chromosome; 5 cases were molecularly confirmed to have a mixed iso- and heteroUPD15 and 1 case each with segmental UPD9pat and segmental UPD22mat; 17 cases were suspected to have a mixed iso- and heteroUPD including 2 cases with small supernumerary marker and 2 cases with mosaic trisomy. For chromosome 15, 12 (92%) of 13 molecularly studied cases had either Prader-Willi or Angelman syndrome. Autosomal recessive disorders were confirmed in seven of nine cases from eight families because of the finding of suspected gene within a ROH. This study demonstrates that ROHs are much more frequent than previously recognized and often reflect parental relatedness, ascertain autosomal recessive diseases or unravel UPD in many cases.European Journal of Human Genetics advance online publication, 13 August 2014; doi:10.1038/ejhg.2014.153.

PMID: 25118026 [PubMed - as supplied by publisher]

High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

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High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

Theor Appl Genet. 2014 Aug 14;

Authors: Brown AF, Yousef GG, Chebrolu KK, Byrd RW, Everhart KW, Thomas A, Reid RW, Parkin IA, Sharpe AG, Oliver R, Guzman I, Jackson EW

Abstract
KEY MESSAGE: A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

PMID: 25119868 [PubMed - as supplied by publisher]

[Detection of mosaic trisomy 9 missed by conventional cytogenetics using SNP-array and fluorescence in situ hybridization.]

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[Detection of mosaic trisomy 9 missed by conventional cytogenetics using SNP-array and fluorescence in situ hybridization.]

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2014 Aug 10;31(4):469-471

Authors: Luo Y, Chen S, Li H, Pan L, Shen M, Jin F, Xu C

Abstract
OBJECTIVE: To detect mosaic trisomy 9 missed by conventional cytogenetics.
METHODS: Peripheral blood genomic DNA from a girl with mental retardation was analyzed using Affymetrix CytoScan (TM) HD array. Fluorescence in situ hybridization (FISH) was also performed on samples from two patients.
RESULTS: The SNP-array analysis has revealed multiple duplications along chromosome 9. FISH analysis showed that, for the peripheral blood sample from one patient, 40 of 100 interphase cells and 15 of 100 metaphase cells carried trisomy 9. For the cord blood sample from another patient, 35 of 100 interphase cells and 10 of 100 cultured cells carried trisomy 9.
CONCLUSION: SNP-array is useful for detecting low-level mosaicism which may be missed by conventional cytogenetics. Combined with karyotype and microarray analyses, FISH is a focused and targeted approach for diagnosing mosaic trisomy. They may provide a useful tool for differentiating pseudomosaicisms from true mosaicisms.

PMID: 25119912 [PubMed - as supplied by publisher]

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