Development and Validation of A High Density SNP Genotyping Array for African Oil Palm.

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Development and Validation of A High Density SNP Genotyping Array for African Oil Palm.

Mol Plant. 2016 Apr 22;

Authors: Kwong QB, Teh CK, Ong AL, Heng HY, Lee HL, Mohamed M, Low JZ, Sukganah A, Chew FT, Mayes S, Kulaveerasingam H, Tammi M, Appleton DR

Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop this whole-genome SNP array, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170,860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium (LD) declined more slowly for the commercial populations (ranging from 120Kb at r(2)=0.43 to 146Kb at r(2)=0.50) when compared with the semi-wild populations (19.5Kb at r(2)=0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on Chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r=0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.

PMID: 27112659 [PubMed - as supplied by publisher]

A patient with constitutional ring 1 chromosome characterized by SNP array CGH.

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A patient with constitutional ring 1 chromosome characterized by SNP array CGH.

Clin Case Rep. 2016 Apr;4(4):442-8

Authors: Saliganan S, Lee J, Wei S

Abstract
We present a male patient with constitutional ring 1 chromosome and subsequent 6 Mb deletion at 1q43q44. The patient displays overlapping clinical features with reported patients with ring 1 chromosome and 1q43q44 microdeletion syndrome. To our knowledge, this is the first patient with ring 1 chromosome characterized by comparative genomic hybridization.

PMID: 27099748 [PubMed]

[Improved identification for 5p deletion syndrome and partial trisomy 11q presented in a fetus by SNP array].

[Improved identification for 5p deletion syndrome and partial trisomy 11q presented in a fetus by SNP array].

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2016 Apr 10;33(2):195-199

Authors: Shi S, Pan G, Yang Y, Yan R, Li W

Abstract
OBJECTIVE: To investigate the prenatal application of single nucleotide polymorphism array (SNP array) in the identification of 5p deletion syndrome with partial trisomy 11q.
METHODS: G-banded karyotyping and SNP array were performed using amniocytes on a fetus with multiple malformations for the identification of chromosome abnormality. Furthermore, karyotyping was carried out on the parental peripheral blood specimens to ascertain the origin of chromosome abnormalities and then fluorescence in situ hybridization (FISH) was also utilized to confirm the results.
RESULTS: Karyotype of amniocyte showed 46, XY, der(5) (?::p15 → qter). SNP array revealed a 13.907 Mb deletion at 5p15.33p15.2 (chr5: 113576-14020561), overlapping the region of 5p deletion syndrome, and a 18.254 Mb duplication at 11q23.3 q25 (chr11: 116684627-134938470), overlapping no known syndrome. Karyotype of the parents showed a normal 46,XX in mother and 46,XY,t(5;11)(p15;q23) in father. Three-color metaphase FISH analysis on paternal peripheral blood specimens also confirmed the paternal karyotyping result.
CONCLUSION: SNP array could uncover 5p deletion syndrome with partial trisomy 11q unidentified by G-banded karyotyping and accurately locate the genomic breakpoints, facilitating the mapping of pathogenic critical regions and the identification of candidate genes, also accumulating research data for genotype-phenotype study.

PMID: 27060314 [PubMed - as supplied by publisher]

A novel hemizygous SACS mutation identified by whole exome sequencing and SNP array analysis in a Chinese ARSACS patient.

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A novel hemizygous SACS mutation identified by whole exome sequencing and SNP array analysis in a Chinese ARSACS patient.

J Neurol Sci. 2016 Mar 15;362:111-4

Authors: Liu L, Li XB, Zi XH, Shen L, Hu ZhM, Huang ShX, Yu DL, Li HB, Xia K, Tang BS, Zhang RX

Abstract
The array of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) has expanded worldwide after the first description in the Charlevoix-Saguenay region of Québec. Here, we report a Chinese ARSACS patient presenting progressive peripheral neuropathy (CMTNS2=15) with horizontal gaze nystagmus and mild spastic gait. Genetic studies including whole exome sequencing (WES), Sanger sequencing and single nucleotide polymorphism (SNP) array analysis revealed a novel hemizygous nonsense mutation (c.11803C>T, p.Gln3935X) of SACS and a 1.33Mb deletion involved in SACS on chromosome 13q12.12 in the patient. Our findings highlight the necessity of SACS mutation screening in the gene panel of inherited peripheral neuropathies, and stress the need of testing copy number variation (CNV) in SACS mutation screening.

PMID: 26944128 [PubMed - in process]

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