Supplemental Information. Whole-Genome Sequencing. of a Healthy Aging Cohort
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1 Cell, Volume 165 Supplemental Information Whole-Genome Sequencing of a Healthy Aging Cohort Galina A. Erikson, Dale L. Bodian, Manuel Rueda, Bhuvan Molparia, Erick R. Scott, Ashley A. Scott-Van Zeeland, Sarah E. Topol, Nathan E. Wineinger, John E. Niederhuber, Eric J. Topol, and Ali Torkamani
2 Wellderly Definition Exclusion Criteria: ICD-9: 149.*172.*, 174.*-198.*, 200.*-239.*, 289.0, 410.*-414.*, 429.2, , 415.1, 325, 344.5, , , , , , , 433.8, 433.9, ,434.10, , , 435.0, 435.1, 435.3, 435.8, , 437.1, 437.6, 437.7, 437.8, 437.9, , , , , , 438.9, 784.3, , V12.51, V12.54,434.91, 250.*, 585.*, V45.11, V56, 39.95, 714.0, 710.0, 710.1, 710.2, 710.3, 710.4, 710.5, 555.*, 556.*, 340, 331.0, 332, 441.*, OR CPT: 566, 4110F, 90935, OR Labs: HgbA1C > 6.5 or Gluc >200 OR Medications: clopidogrel, plavix, prasugrel, effient, ticagrelor, brilinta, cilostazol, pletal, dipyridamole, aggrenox, persantine, ticlopidine, ticlid, donepezil, aricept, rivastigmine, exelon, galantamine, nivalin, razadyne, reminyl, lycoremine, cognex, tacrine `````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````` Notes: Any Cancer (including polycythemia (289.0) and Melanoma (172.*, V10.82); excluding basal or squamous cell skin cancer). (149.*172.*, 174.*-198.*, 200.*-239.*) Coronary Artery Disease (411.*-414.*, 429.*)/Myocardial Infarction (410.*) (CPT 566 anesthesia for direct CABG w/o pump oxygenator, 4110F internal mammary artery graft performed for primary, isolated CABG) Stroke (325, 344.5, , , , , , , 433.8, 433.9, ,434.10, , , 435.0, 435.1, 435.3, 435.8, , 437.1, 437.6, 437.7, 437.8, 437.9, , , , , , 438.9, 784.3, , V12.51, V12.54,434.91) /TIA (435.9) Deep Vein Thrombosis (453.40)/Pulmonary Embolus (415.1) Chronic Renal Disease (585.*)/Hemodialysis (V45.11, V56, 39.95, cpt: 90935, 90937) Significant Auto-immune/Inflammatory conditions such as (Rheumatoid Arthritis (714.0, Lupus & other diffuse diseases of connective tissue (710.0), Crohn s (555.*), Ulcerative colitis (556.*), MS (340) etc.) Alzheimer (331.0)/Parkinson (332) Diabetes (Hemoglobin A1C > 6.5 % or fasting glucose >126 mg/dl or treated with oral diabetic medication or insulin if known) Aortic or Cerebral Aneurysm (441.*, 437.3) Anti-platelet agents, not including aspirin (ex.:clopidogrel/plavix, dipyridamole/aggrenox/ persantine, ticlopidine/ticlid) Cholinesterase inhibitor for Alzheimer disease (i.e. donepezil/aricept) Allowed Basal/Squamous Skin Cancer Definition: Histology:
3 Squamous cell carcinoma in situ, NOS Squamous cell carcinoma, NOS Sq. cell carcinoma, keratinizing, NOS, in situ Squamous cell carcinoma, keratinizing, NOS Sq. cell carcinoma, lg cell non-ker., situ Squamous cell carcinoma, lg cell, nonkeratinizing, NOS Squamous cell carcinoma, sm cell, nonkeratinizing Squamous cell carcinoma, spindle cell Squamous cell carcinoma, adenoid Squamous cell carcinoma in situ, question stromal inv Squamous cell carcinoma, microinvasive Squamous intraepithelial neoplasia, grade III Squamous cell carcinoma with horn formation Queyrat erythroplasia Bowen disease Lymphoepithelial carcinoma Basaloid squamous cell carcinoma Squamous cell carcinoma, clear cell type Basal cell tumor Basal cell carcinoma, NOS Basal cell carcinoma, multifocal superficial Basal cell carcinoma, infiltrating, NOS Basal cell carcinoma, fibroepithelial Basosquamous carcinoma Metatypical carcinoma Intraepidermal epithelioma of Jadassohn Basal cell carcinoma, nodular Adenoid basal carcinoma AND Primary Site: C440 - Skin of lip C441 - Eyelid C442 - External ear C443 - Skin of other/unspecified parts of face, NOS C444 - Skin of scalp and neck C445 - Skin of trunk C446 - Skin of upper limb and shoulder C447 - Skin of lower limb and hip C448 - Skin, overlapping lesion C449 - Skin, NOS
4 Gene Lists Considered for Pathogenic Variant Burden Analysis Hereditary Dementia: ALS2, ANG, APP, ATP13A2, ATXN2, C9orf72, CHGB, CHMP2B, DCTN1, DNAJC6, EIF4G1, ERBB4, FBXO7, FIG4, FUS, GIGYF2, GRN, HNRNPA1, HTRA2, LRRK2, MAPT, MATR3, NEFH, OPTN, PARK2, PARK7, PFN1, PINK1, PLA2G6, PRNP, PRPH2, PSEN1, PSEN2, SETX, SIGMAR1, SNCA, SOD1, SORL1, SPG20, SYNJ1, TARDBP, TREM2, UBQLN2, VAPB, VCP, VEGFA, VPS35, VPS54 Hereditary Cancer: AIP, APC, ARID1A, ARID1B, ATM, AXIN2, BAP1, BARD1, BHD, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, BTBD12, BUB1B, C17orf68, CDC73, CDH1, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CHEK2, CREBBP, CYLD, DDB2, DICER1, DKC1, DNMT3A, EP300, EPCAM, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, ERCC8, EXO1, EXT1, EXT2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FH, FLCN, GPC3, HNF1A, MAX, MEN1, MINPP1, MITF, MLH1, MLH3, MRE11A, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NHP2, NOP10, PALB2, PAX3, PHOX2B, PMS1, PMS2, POLD1, POLE, POLE1, POLH, PRF1, PRKAR1A, PTCH1, PTCH2, PTEN, PTPN11, RAD50, RAD51, RAD51C, RAD51L3, RB1, RECQL4, SBDS, SDHA, SDHB, SDHC, SDHD, SETBP1, SMAD4, SMARCA4, SMARCB1, SMARCE1, SOS1, SPRED1, STK11, SUFU, TERC, TERT, TET2, TGFBR1, TGFBR2, TINF2, TMEM127, TP53, TRAD, TSC1, TSC2, VHL, WRAP53, WRN, WT1, XPA, XPC Common Monogenic Disorders: ACTA2, ACTC1, APC, APOB, BRCA1, BRCA2, CACNA1S, COL3A1, DSC2, DSG2, DSP, FBN1, GLA, KCNH2, KCNQ1, LDLR, LMNA, MEN1, MLH1, MSH2, MSH6, MUTYH, MYBPC3, MYH11, MYH7, MYL2, MYL3, MYLK, NF2, NTRK1, PCSK9, PKP2, PMS2, PRKAG2, PTEN, RB1, RET, RYR1, RYR2, SCN5A, SDHAF2, SDHB, SDHC, SDHD, SMAD3, STK11, TGFBR1, TGFBR2, TMEM43, TNNI3, TNNT2, TP53, TPM1, TSC1, TSC2, VHL, WT1
5 Supplemental Table S1. Variant Filtration, Related to Experimental Methods Total Wellderly Cohort ITMI Cohort Allele Frequency <1% 1-5% >5% <1% 1-5% >5% Initial High Quality Variants 56,887,341 24,439,069 3,777,909 7,739,481 30,472,344 3,843,365 7,772,707 General Variant Filters (Removed Variants) Clustered Variants 1,305, , , , , , ,755 >10% Missing Genotypes Median coverage <10X or >100X 9,526,728 3,514,510 1,244,089 1,822,760 4,412,033 1,271,645 1,848,517 2,622, , , ,672 1,107, , ,803 Simple Repeats 3,425,306 1,363, , ,471 1,701, , ,092 Homopolymers 4,085,185 1,714, , ,790 2,077, , ,350 Segmental Duplications 1,943, , , , , , ,475 Microsatellite Repeats 79,408 26,231 13,758 11,476 34,135 14,429 11,856 RepeatMasker 2,940,350 1,135, , ,269 1,437, , ,136 Hardy-Weinberg Equilibrium 277,589 77,243 27, ,294 85,218 29, ,297 Non-unique 36mers 16,804,012 7,146,073 1,422,546 2,227,868 8,896,445 1,450,058 2,248,024 Total (Remaining Variants) Total Variants Remaining 33,457,609 14,584,108 1,783,087 4,346,334 18,200,688 1,812,835 4,350,062 Uncommon (AF<5%) Variant Filters (Removed Variants) Allele Depth 9,252,058 3,787,460 1,637, ,932,158 1,671,807 0 Total (Remaining Variants) Total Variants Remaining 24,205,551 10,796, ,098 4,346,334 13,268, ,028 4,350,062 The number of variants removed per applied filter, broken down into rare (<1%), uncommon (1-5%) and common (>5%) variants. The cumulative total number of remaining variants is provided in the last row.
6 Supplemental Table S2. Variant Characteristics, Related to Experimental Methods Wellderly Cohort ITMI Cohort # Samples AF <1% 1-5% >5% <1% 1-5% >5% Total # of SNPs 10,256, ,656 4,075,203 13,105, ,673 4,078,917 # Nonsense 2, , # Splice-Site 1, , # Missense 92, , , ,764 # Synonymous 53, ,513 67, ,487 # Intronic 4,602,856 57,242 1,732,378 5,876,739 55,588 1,733,611 # Intergenic 5,504,854 76,092 2,311,225 7,036,963 73,777 2,313,719 Total # of INDELS 540,074 10, , ,022 10, ,145 # Frameshift 2, # In-frame 1, # Splice-Site # Intronic 247,887 4, ,615 70,177 4, ,626 # Intergenic 288,411 5, ,056 91,577 5, ,064 The number of variants identified in each cohort, broken down by coding impact, and allele frequency class - rare (<1%), uncommon (1-5%) and common (>5%) variants.
7 Supplemental Table S7. Variants, Related to Figure 4 Position chr4: A>C chr4: G>A chr4: G>A chr4: T>C chr4: C>A chr4: T>C chr4: G>A chr4: T>C chr4: G>A cdna Change c.1866t>g c.1559c>t c.1204c>t c.1174a>g c.673g>t c.512a>g c.347c>t c.179a>g c.143c>t Coding Change p.h622q p.p520l p.r402c p.t392a p.g225c p.n171s p.s116l p.q60r p.s48f Wellderly Alleles ITMI Alleles Frequency in ExAC % % % % % The variants observed in this study is displayed with the cdna and protein impact, counts per cohort, and allele frequency in the Exome Aggregation Consortium cohort.
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