GBinsight Sample Name: GB4411 Race: Gender: Female Reason for Testing: Type 2 diabetes, early onset MRN: 0123456789 Specimen: Saliva Received: 07/26/2016 Test ID: 113-1487118782-4 Test: Type 2 Diabetes Comprehensive Panel Referring Doctor: Dr. William Smith Referring Facility: GB HealthWatch GENETIC ANALYSIS REPORT SUMMARY This individual's genomic DNA was sequenced using next generation sequencing (NGS) at the regions targeted by GBinsight Panels. The targeted regions cover thirteen million base pairs (bp), including 327 exons and selected single nucleotide polymorphisms loci in 639 genes. More than 99% of targeted positions were sequenced at 100X coverage or higher, resulting in 1,338 variants identified compared to the reference genome. These data were analyzed with a bioinformatics pipeline developed by GB HealthWatch (see Methodology below). Results are summarized here with further details on subsequent pages. A. Pathogenic and Likely Pathogenic Variants 0 identified This test did NOT identify pathogenic or likely pathogenic genetic variants that have been reported in the ClinVar database or in peer-reviewed literature. B. Variants of Uncertain Significance with Possible High-Impact to Disease Risk 1 identified This test identified 1 low frequency variant with predicted protein or transcript damage. Its pathogenicity or effect on disease risk is unknown or has not been assessed. Disease (Inheritance) Gene Transcript Zygosity Variant Classification Minor Allele Freq Global / EAS* Maturity-onset diabetes of the young, type IX (Autosomal dominant) Diabetes mellitus, type 2 (Polygenic risk factor) PAX4 NM_006193.2 Heterozygous c.574c>a (p.arg192ser) Likely high risk (Protein Damaging) <1% / 2% * Minor allele frequency estimated from 1000 Genomes Phase 3 Database. Global population / subpopulation. C. Polygenic Disease Risk The type 2 diabetes risk score is calculated from genes and genomic regions included in the GBinsight Type 2 Diabetes Comprehensive Panel. The risk score is expressed as relative risk to the individual s reference population. Biological pathways associated with type 2 diabetes risk are also scored. 53 out of 1,338 variants identified from this individual's genomic DNA are selected as risk variants and used in risk score calculations. Disease Risk Score Relative Risk Reference Population Type 2 diabetes 90 High Risk Disease Related Pathway Defective beta cell development (MODY genes) Defective beta cell development (non-mody genes) 85 High Risk 10 Low Risk
Risk Score Relative Risk Reference Population Disease Related Pathway Impairment of glucose sensor and insulin release 5 Low risk Impairment of insulin signaling (organ resistance) 55 Average risk Impairment of glucagon signaling 50 Average risk Hypertriglyceridemia (defective in lipid clearance, utilization, biosynthesis or storage) 70 Moderate risk 80 High risk Cellular senescence and apoptosis 10 Low risk Low cholesterol 95 High risk D. Pharmacogenomic Associations 2 identified This test identified the following pharmacogenomic associations: Drug Risk and Dosing Information Metformin Sulfonylurea agent Decreased glycemic response to metformin. Increased glycemic response to sulfnylurea oral hypoglycemic agent gliclazide. Carter Ma, Ph.D. Bioinformatics Scientist Mendel Roth, Ph.D. Genetics/Molecular Biologist GBinsight Team
DETAILED VARIANT INFORMATION A. Type 2 Diabetes Risk Variants Pathway Gene Variant SNP Genotype Zygosity Consequence Significance Defective beta cell development (MODY genes) Defective beta cell development (non- MODY genes) PAX4 c.574c>a(p.arg192ser) rs3824004 G/T HET probably damaging Likely high risk PAX4 c.962a>c(p.his321pro) rs712701 T/G HET benign Risk factor CDKAL1 c.371+30101a>g rs7756992 A/G HET intron-variant Risk factor GLIS3 c.-98-5224g>c rs7020673 C/G HET intron-variant Risk factor HHEX c.92705802c>t rs5015480 C/T HET nc-transcript-variant Risk factor IGF1 c.-1410t>c rs35767 A/G HET upstream-variant-2kb Risk factor Glucose sensor and insulin release G6PC2 c.441-26t>c rs560887 C/C HOM intron-variant Protective SLC30A8 c.826c>t (p.arg276trp) rs13266634 C/T HET benign Protective KCNJ11 c.67a>g (p.lys23glu) rs5219 T/C HET benign Risk factor ABCC8 c.4105g>t (p.ala1369ser) rs757110 C/A HET benign Risk factor ADCY5 C2CD4A CRY2 c.1135-23023a>g rs2877716 C/C HET intron-variant Risk factor g.62090956t>c rs4502156 T/C HET nc-transcript-variant Risk factor c.278+3835a>c rs11605924 A/C HET intron-variant Risk factor Insulin signaling (organ resistance) TRPM6 c.4750a>g (p.lys1579glu) rs2274924 T/C HET possibly damaging Risk factor ADIPOQ g.186831906g>a rs10937273 G/A HET nc-transcript-variant Risk factor DGKB g.15024684g>t rs2191349 T/T HOM nc-transcript-variant Risk factor IRS1 g.226229029t>c rs2943641 C/C HOM nc-transcript-variant Risk factor Hypertriglyceridemia APOA5 c.*158c>t rs2266788 G/A HET utr-variant-3-prime Risk factor FADS1 c.1248+52a>g rs174547 T/C HET intron-variant Risk factor GCKR c.1337t>c (p.leu446pro) rs1260326 T/C HET possibly damaging Risk factor LIPC g.58391167a>g rs1532085 A/G HET intron-variant Risk factor LPL ZPR1 APOC3 c.1421c>g (p.ser474ter) rs328 C/G HET stop-gained Risk factor c.*724c>g rs964184 G/C HET utr-variant-3-prime Risk factor c.*40g>c rs5128 G/C HET utr-variant-3-prime Risk factor LIPC g.58386313c>t rs10468017 C/T HET intron-variant Risk factor LPL PPARGC1A PROX1 c.1323-187a>g rs326 A/G HET intron-variant Risk factor c.1444g>a (p.gly482ser) rs8192678 C/T HET benign Risk factor g.213985913t>c rs340874 T/C HET intron-variant Risk factor ADRB2 c.46a>g (p.arg16gly) rs1042713 A/A HOM benign Risk factor GHRL c.178c>a (p.leu60met) rs696217 G/T HET probably damaging Risk factor MC3R c.130g>a (p.val44ile) rs3827103 G/A HET benign Risk factor MC4R g.60183864t>c rs17782313 T/C HET nc-transcript-variant Risk factor
Detailed Variant Information, Type 2 Diabetes Risk Variants: (continued) Pathway Gene Variant SNP Genotype Zygocity Consequence Significance ENPP1 c.*1043a>g rs7754561 A/G HET utr-variant-3-prime Risk factor LEPR c.326a>g (p.lys109arg) rs1137100 G/G HOM benign Risk factor NEGR1 g.72372846a>g rs1993709 G/G HOM intron-variant Protective TMEM18 g.634905t>c rs6548238 C/C HOM noncoding Protective UCP2 c.164c>t (p.ala55val) rs660339 G/A HET benign Risk factor UCP2 c.-1245g>a rs659366 C/T HET upstream-variant-2kb Risk factor ADCY3 g.24935139t>c rs713586 T/C HET nc-transcript-variant Risk factor KCTD15 g.33818627a>g rs29941 A/G HET nc-transcript-variant Risk factor SDC3 c.986c>t (p.thr329ile) rs2282440 A/A HOM benign Risk factor SEC16B c.1881+177a>g rs2282440 T/C HET intron-variant Risk factor Cellular senescence and apoptosis Low cholesterol RASGRP1 c.221-4300a>g rs7403531 T/C HET intron-variant Risk factor CDKN2A g.22134095t>c rs10811661 C/C HOM nc-transcript-variant Protective PCSK9 Novel Variant 1:55521802_C/ CACCGCTGCCGGCA (p.val312fs) C/CACCGCT GCCGGCA HET Loss-of-function Likely high risk PCSK9 c.158c>t (p.ala53val) rs11583680 C/T HET benign Risk factor APOB c.5768a>g (p.his1923arg) rs533617 T/C HET probably damaging Risk factor APOB g.21166787t>g rs4635554 T/G HET nc-transcript-variant Risk factor CELSR2 c.*919g>t rs12740374 G/T HET utr-variant-3-prime Protective HMGCR c.1368+1176a>t rs12654264 A/T HET intron-variant Risk factor ABCA1 c.656g>a (p.arg219lys) rs2230806 C/T HET benign Risk factor ABCA1 c.2473g>a (p.val825ile) rs2066715 T/T HOM benign Risk factor APOE c.-24+69c>g (p.asn14lys) rs440446 C/G HET missense Protective B. Pharmacogenomic Associations Molecular Drug Gene Variant SNP Genotype Zygosity Consequence Significance Metformin Sulfonylurea agent Gliclazide C11orf65 c.82-5471g>t rs11212617 A/A HOM intron variant Decreased response ABCC8 c.4105g>t (p.ala1369ser) rs757110 C/A HET missense (benign) Increased response
METHODOLOGY Genomic sequencing is performed using next generation sequencing on the Illumina HiSeq platform. GBinsight panel-targeted positions were sequenced at 100X coverage or higher. Paired-end 100bp reads are aligned to the NCBI reference sequence (GRCh37) using the Borrows-Wheeler Algorithm (BWA) and variant calls are made using the Genomic Analysis Tool kit (GATK). Variants are subsequently filtered to identify: (1) variants classified as pathogenic or likely pathogenic in the public database; (2) nonsense, frameshift and +/- 1,2 splice-site variants that are novel or have a minor allele frequency <1% in the 1000 Genomes Project database; (3) missense variants that are predicted to be protein-damaging by at least two of three algorithms of PolyPhen-2, Provean and SIFT; (4) variants in coding and non-coding regions that were previously reported as risk factors by either genome-wide association studies (GWAS) or in the literature; (5) variants with clinical significance information derived from the GB HealthWatch internal testing and analysis database. GBinsight follows the standards and guidelines for the interpretation of sequence variants set forth by the American College of Medical Genetics (ACMG). In addition to classifying variants into pathogenic and likely pathogenic categories recommended for Mendelian inheritance diseases, this report also provides an estimation of risk score for polygenic diseases. The risk score is calculated using a proprietary algorithm developed by GB HealthWatch. For more information, please visit: https://www.gbhealthwatch.com/gbinsight/how-it-works.php. The DNA sequencing was performed by the Otogenetics Corporation, a CLIA certified and medical licensed molecular diagnostic laboratory in Atlanta, Georgia, USA. Alignment, variant calling, data filtering and interpretation are performed by GB HealthWatch, San Diego, California, USA. This test is for research purposes only. The test has not been cleared or approved by the US Food and Drug Administration (FDA) or the FDA has determined that such clearance or approval is not necessary. LIMITATIONS It should be noted that this test does not sequence all bases in a human genome and not all variants have been identified or interpreted. Tandem repeat expansion, translocations and large copy number events are currently not reliably detected by NGS. Furthermore, not all disease-associated genes have been identified and the clinical significance of variants in many genes is not well understood. It is recommended that genomic sequence data be used only as a reference for investigating potential causality of phenotype and not used for diagnosing a particular disease. If phenotype is not consistent with the genetic risk assessment provided by this test, then other genetic variants that are not detectable by this test should be suspected. Alternatively, non-genetic factors, such as diet and exercise, should be considered as risk-modifying.