Sample_160512_Hiseq1B_l7_M
The aim of this study is screening the functional classification and                 disease risks associated in the study group which is exposed to environmental                 obesogen by next generation sequencing (NGS) technique. A totally 9 females                 classified according to their BPA concentration ranged 1 to 2.6 ng/ml and all                 participants were assessed BPA, lipid profile, and FBS. The genomic DNA was                 extracted from blood and the whole genome of 9 females was sequenced using a HiSeq                 2000 Genome Analyzer (Illumina, San Diego, CA, USA). The bioinformatics analyses                 were performed; the filtered reads were aligned onto the hg38 human reference using                 BWA-sampe and BWA-ALN with default option, SAM files were converted to BAM file                 using samtools 0.1.19 also samtools used for sorting the resulted BAM file, to                 remove PCR duplicated reads, MarkDuplicate subroutine in Picard v1.9.2 was used, the                 variants were called by GATK UnifiedGenotyper with -mbq 30 -stand_emit_conf 50                 -stand_call_conf 50 options, Also VariantFiltration from GATK was performed using                 --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore                 > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0"                 --filterName "SNP_FILTER_1" options, Annotation done using ANNOVAR using the VCF                 file as input with -buildver ${GENOME} \ -out ${ID} \ -remove \ -protocol                 knownGene,refGene,cosmic70,avsnp147 \ -operation g,g,f,f \ -nastring . \ -vcfinput                 options. The type and genomic regions of variants were annotated using snpEff v4.3i.                 To predict mutations which make possible functional altering amino acid changes,                 Provean program was used. These protein damaging mutations were further annotated                 with OMIM and ClinVar.
Submitters
Elsayed Hegazy,  Asmaa ElFiky, Sumio Sugano, Terumi Horiuchi, Abe Kazumi and Mahmoud ElHefnawi
Submitting Organization
School of Communication  Information Technology, Center for Informatics Science, Nile University, Giza, Egypt
Submitting Organization
National Research Centre, Cairo, Egypt
Submitting Organization
The Institute of Medical Science, University of Tokyo, Japan
Submitting Organization
Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan