Erratum to: high-resolution SNP array analysis of patients with developmental disorder and normal array CGH result.
BMC Med Genet. 2014;15(1):124
Authors: Siggberg L, Ala-Mello S, Linnankivi T, Avela K, Scheinin I, Kristiansson K, Lahermo P, Hietala M, Metsähonkala L, Kuusinen E, Laaksonen M, Saarela J, Knuutila S
PMID: 25409779 [PubMed - as supplied by publisher]
Three gangliogliomas: Results of GTG-banding, SKY, genome-wide high resolution SNP-array, gene expression and review of the literature.
Neuropathology. 2014 Nov 6;
Authors: Xu LX, Holland H, Kirsten H, Ahnert P, Krupp W, Bauer M, Schober R, Mueller W, Fritzsch D, Meixensberger J, Koschny R
According to the World Health Organization gangliogliomas are classified as well-differentiated and slowly growing neuroepithelial tumors, composed of neoplastic mature ganglion and glial cells. It is the most frequent tumor entity observed in patients with long-term epilepsy. Comprehensive cytogenetic and molecular cytogenetic data including high-resolution genomic profiling (single nucleotide polymorphism (SNP)-array) of gangliogliomas are scarce but necessary for a better oncological understanding of this tumor entity. For a detailed characterization at the single cell and cell population levels, we analyzed genomic alterations of three gangliogliomas using trypsin-Giemsa banding (GTG-banding) and by spectral karyotyping (SKY) in combination with SNP-array and gene expression array experiments. By GTG and SKY, we could confirm frequently detected chromosomal aberrations (losses within chromosomes 10, 13 and 22; gains within chromosomes 5, 7, 8 and 12), and identify so far unknown genetic aberrations like the unbalanced non-reciprocal translocation t(1;18)(q21;q21). Interestingly, we report on the second so far detected ganglioglioma with ring chromosome 1. Analyses of SNP-array data from two of the tumors and respective germline DNA (peripheral blood) identified few small gains and losses and a number of copy-neutral regions with loss of heterozygosity (LOH) in germline and in tumor tissue. In comparison to germline DNA, tumor tissues did not show substantial regions with significant loss or gain or with newly developed LOH. Gene expression analyses of tumor-specific genes revealed similarities in the profile of the analyzed samples regarding different relevant pathways. Taken together, we describe overlapping but also distinct and novel genetic aberrations of three gangliogliomas.
PMID: 25376146 [PubMed - as supplied by publisher]
FISH analysis of PTEN in endometrial carcinoma. Comparison with SNP arrays and MLPA.
Histopathology. 2014 Sep;65(3):371-88
Authors: Maiques O, Cuevas D, García Dios DA, Coenegrachts L, Santacana M, Velasco A, Romero M, Sónia G, Lambrechts D, Dolcet X, Amant F, Matias-Guiu X
AIMS: To check the usefulness of a standardized protocol of PTEN FISH in 31 endometrial carcinomas (ECs) in comparison with SNP array (SNPA), multiplex ligation-dependent probe amplification (MLPA), and immunohistochemistry.
METHODS AND RESULTS: Fluorescence in-situ hybridization analysis showed two PTEN copies in 17 cases, three copies in nine cases, hemizygous deletion in two cases, and diverse cell populations with different PTEN copy number in three cases. A good correlation was seen between FISH and SNPA, particularly in cases with three copies. FISH identified two cases with entire deletion of chromosome 10, but did not identify a focal deletion of PTEN. Five cases with PTEN deletion and duplication of the second allele by SNPA were interpreted as normal by FISH. Concordance between FISH and MLPA was seen in 15 cases with two copies, and in two cases with PTEN deletion. Six cases were interpreted as amplified by MLPA, but showed polyploidy by FISH. FISH was superior to SNPA and MLPA in assessing the tumours with diverse cell populations with different PTEN copies.
CONCLUSIONS: The results show good concordance between FISH, SNPA and MLPA. SNPA was superior in tumours with deletion of one copy and duplication of the second allele. FISH was superior in assessing tumour heterogeneity.
PMID: 25353038 [PubMed - in process]
Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance.
BMC Res Notes. 2014 Oct 22;7(1):747
Authors: Kumar P, Al-Shafai M, Al Muftah WA, Chalhoub N, Elsaid MF, Aleem AA, Suhre K
BACKGROUND: With diminishing costs of next generation sequencing (NGS), whole genome analysis becomes a standard tool for identifying genetic causes of inherited diseases. Commercial NGS service providers in general not only provide raw genomic reads, but further deliver SNP calls to their clients. However, the question for the user arises whether to use the SNP data as is, or process the raw sequencing data further through more sophisticated SNP calling pipelines with more advanced algorithms.
RESULTS: Here we report a detailed comparison of SNPs called using the popular GATK multiple-sample calling protocol to SNPs delivered as part of a 40x whole genome sequencing project by Illumina Inc of 171 human genomes of Arab descent (108 unrelated Qatari genomes, 19 trios, and 2 families with rare diseases) and compare them to variants provided by the Illumina CASAVA pipeline. GATK multi-sample calling identifies more variants than the CASAVA pipeline. The additional variants from GATK are robust for Mendelian consistencies but weak in terms of statistical parameters such as TsTv ratio. However, these additional variants do not make a difference in detecting the causative variants in the studied phenotype.
CONCLUSION: Both pipelines, GATK multi-sample calling and Illumina CASAVA single sample calling, have highly similar performance in SNP calling at the level of putatively causative variants.
PMID: 25339461 [PubMed - as supplied by publisher]