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

2. 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.

3. Chromosome X/Y coverage
Male ?
Female

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

5. 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

6. 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

7. 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

8. 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

9. 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!).

10. 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

11. Carriers per geographic regions