Armenian Genome Project

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Presentation transcript:

Armenian Genome Project Hane Lee, PhD Clinical Genomics Center Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles

Variant Stats Sequencing quality was good and consistent. SNVs SNVs dbSNP132 rate (%) dbSNP132 concordance rate (%) ti/tv ratio (known) het/homo ratio (known) ti/tv ratio (novel) het/homo ratio (novel) INDELs From Seq data SN03740-P 20,459 96.0 99.8 3.2 1.5 2.9 48.0 1,165 Female SN03725-P 20,480 3.0 20.6 1,175 Male SN03729-P 20,581 3.1 37.7 1,184 SN03733-P 20,324 95.8 1.4 2.7 19.2 1,179 SN03744-P 20,071 96.1 99.9 19.7 1,135 SN03747-P 20,074 96.2 17.3 1,206 SN03751-P 20,110 3.4 19.4 1,215 SN03752-P 20,441 96.3 2.6 20.4 1,148 SN03758-P 20,262 3.3 18.4 1,154 SN03780-P 20,238 2.8 21.7 1,106 SN03781-P 19.8 SN03771-P 20,427 95.7 21.1 1,160 SN03774-P 20,299 21.6 1,159 SN03776-P 20,403 95.9 2.5 18.0 SN03759-P 20,163 20.5 1,131 SN03763-P 20,327 25.8 SN03767-P 20,350 14.4 1,169 SN03785-P 20,032 35.8 1,109 SN03786-P 20,449 19.1 1,134 SN03787-P 19,688 24.8 1,112 Sequencing quality was good and consistent.

Chromosome X/Y coverage Male ? Female

Number of SNVs *African American population includes samples with mixed ethnicity

Genetic Ancestry and Population Structure Population Structure of 172 individuals sequenced as part of UCLA Clinical Exome Sequencing project. Evaluated 15,000 Single nucleotide variants MAF > 0.05

Genetic Ancestry and Population Structure Population Structure of 172 individuals sequenced as part of UCLA Clinical Exome Sequencing project. Evaluated 15,000 Single nucleotide variants MAF > 0.05

Genetic Ancestry and Population Structure with regional information from Armenia Population Structure of 104 individuals sequenced as part of UCLA Clinical Exome Sequencing project. Evaluated 10,000 Single nucleotide variants MAF > 0.05

Genetic Ancestry and Population Structure with regional information from Armenia Population Structure of 104 individuals sequenced as part of UCLA Clinical Exome Sequencing project. Evaluated 10,000 Single nucleotide variants MAF > 0.05

Rare Variants in Genes Affecting Ashkenazi Jewish individuals Identified 47 SNPs in (FANCC, MEFV, GBA, GNE, PAH, ASPA, HEXA) in 248 CES exomes (20 Armenians included) 23/47 variants with <1% MAF in exAC 13/23 variants classified by Clinvar (Pathogenic, Likely Pathogenic, Conflicting interpretation, Not Provided) or were not classified in Clinvar. Minor allele frequency estimated for Armenian group (! Too low for accuracy!).

Carrier proportion of MEFV and PAH mutations in Armenians 5 of 13 variants from above found in Armenian cohort Familial Mediterranean Fever (MEFV) variants and Armenian carriers Phenylketonuria (PAH) variants and Armenian carriers # with no mutations # carriers # homozygotes

Carriers per geographic regions