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. Author manuscript; available in PMC: 2016 Dec 1.
Published in final edited form as: Gastroenterology. 2015 Sep 5;149(7):1872–1883.e9. doi: 10.1053/j.gastro.2015.08.052

Table 1.

uFCRC Patient High Quality Variants, DSB Phenotypes, Polyp Histories, and Family Histories.

Patient
ID #
HQ Variants γH2AX + Flow
Cytometry
Polyps (No
or type)
Family History of Neoplasia
111797 CHAF1B Aph, UV ↑S No Sis/CRC@41; M/CRC@72; MA/Ovar@63; MGF/Gastric@46; MGM/Panc@72
118294 SHPRH Aph, Campt ↑S No F/pols@72; M/ut@71; M/BCC@76; MC/Laryn@51; MGF/Panc@69; PA/Br&Skin@33; PGF/Esoph@51
120713 (Pt1) WRN; ERCC6 No RX, Aph, Campt, UV, Etop ↑G2/M No F/Blad; F&M/BCC@40s; Bro/BCC@50; Sis/CRC@48; PC1xR/Br@50; PC1xR/Ovar@40s
122517 POLD1; MCM10; MPG; SKA1 Aph, Campt Nl mult Sis/pols@37; F/CRC@41; PA/CRC@27; PGM/CRC@62; PGF/IntestSarc@31; PGF Sis/Sig@62
123000 SPAG5 BRD4 Aph, UV NT No Bro/pols@64; Bro/pols@67; MU/CRC@60s; MA/CRC@60s; MC/CRC@68; F/CRC@79
123006 MASTL UV ↑S No No
123163 DYNC1H1 CHAF1A Nl Nl No MA/Melan@45; A/Br@61; A/CRC@49; A/pols@58; Neph/pols@33; GM/CRC@63; GA/lymph@73; 4 1stCs1xR/CRC; GA/Uter@52; GA/Br@80,CRC; C/CRC@55
123320 MSH2 UV ↑G2/M No No
124744 FANCL Nl Nl No Sis/pols@51; Bro/pols@56; Sis/pols@41; Sis/pol@39; Bro/pols@36; N/pols@27; M/Adeno@67; MA/CRC@51,pols@56; MGF/pols@47; F/CRC in pols@56; PA/CRC&pols@47; PC/CRC@58
125380 [POLK]* No Rx, Aph, UV ↑S, G2/M No MGA/Esoph; MGA/Gastric; MCA/CRC; F/Pros@63; F/pols@67; F/Panc@70; PU/pols
125659 EEPD1 UV Nl No M/pol@70s; MU/Panc@53; PGF/GI@89; PGM/Liver@63
126780 ERCC2 No Rx, Aph Nl No M/Panc@60; MU/Gastric@60; MU/unknown@50; F/CRC@60; F/pols
126875 ANAPC10 No Rx, Aph Aph: ↓S ↑G2/M No S/Bileduct@41, MU/CRC@50s; PU/CRC@50s; MSH2 mutation in PA/Gastric@60s; pt – for MSH2
127581 CTC1 No Rx, Aph Aph: ↑G2/M No M/CRC@58; PGF/CRC@58
129338 None Nl ↑S, G2/M mult@50s MU/pols&CRC@79; Son/Blad@50s; Son/pols@50s; MU/pols@75; MC/Br@43; MU/pols&CRC@63; MC/pols@60s; MA/pols@75; MGM/Panc@65; MA/CRC@60s&Endom&Ovar; Son/CRC
132231 C19Orf40 Nl Nl 2 adv Bro/pols@50
132406 DDX11*; LIG1; Aph, UV NT 1 ser Bro/CRC&pols@40,55; M/pols@50s&CRC@72
132667 LIG3 Aph, UV NT >5 serr adv@<50 Bro/CRC@44; MU/Canc@70s; MU/Stom/Esopha@50s, MA/Panc@70s; MC/Brain@57; MC/CRC@45; MC/CRC@52; MU/Canc@85; MC/Lung@52
133012 POLD3 No Rx, Aph Nl 3 adv M/pols@60s; P1/2Sis/pols@32; PU/pols@50
134321 None Nl Nl 1 adv NA

HQ Variant: variant with GO annotation of DNA replication, DNA repair, checkpoint, mitotic, or mitosis; reported in < 1/100 exomes; and scoring > 0.95 on the current PolyPhen2 program and (+) by 2/3: SIFT, Provean, and MutationAssessor programs. γH2AX+: conditions under which the patient's cells showed statistically greater staining than the control or controls: 1) higher than the optimized discriminator line for aphidicolin or UV treatment (Fig 2); 2) higher than all controls for the No Rx condition; or 3) statistically greater than its specific matched controls (Pt1 and Pt2). Flow Cytometry: replicative phases in which the % of patient’s cells was > 20% higher than the controls. Polyps: polyps in the patients - known number and nature are listed (mult: >3, adv: advanced (> 1 cm, high grade dysplasia, or villous histology), ser: serrated adenomas. NT: not tested, Nl: normal. Family history of neoplasia: F: father, M: mother, Sis: sister, Bro: brother, MA: maternal aunt, MU: maternal uncle, PU: paternal uncle, MC: maternal cousin etc./organ site@age at diagnosis, Pols: polyps.

*

The POLK variant was predicted to be dysfunctional by PP2 and MutationAssessor but narrowly not by SIFT, and hence is technically not HQV (see main text).

*

The DDX11 variant sequence was also found in 2 other strong homology regions on chr12 and was flagged with low quality metrics in ExAC.