PMID: 25157968

Prospective enterprise-level molecular genotyping of a cohort of cancer patients.

The Journal of molecular diagnostics : JMD
LE MacConaill, E Garcia, P Shivdasani, M Ducar, R Adusumilli, M Breneiser, M Byrne, L Chung, J Conneely, L Crosby, LA Garraway, X Gong, WC Hahn, C Hatton, PW Kantoff, M Kluk, F Kuo, Y Jia, R Joshi, J Longtine, A Manning, E Palescandolo, N Sharaf, L Sholl, P van Hummelen, J Wade, BM Wollinson, D Zepf, BJ Rollins, NI Lindeman
2014-11

226 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
3-41266112-T-G CTNNB1 c.109T>G p.Ser37Ala Missense 3/16 -
3-41266112-T-C CTNNB1 c.109T>C p.Ser37Pro Missense 3/16 -
7-140453132-T-G BRAF c.1803A>C p.Lys601Asn Missense 15/18 -
7-140481397-C-A BRAF c.1411G>T p.Val471Phe Missense 11/18 -
9-80409488-T-A GNAQ c.626A>T p.Gln209Leu Missense 5/7 -
12-25398281-C-G KRAS c.38G>C p.Gly13Ala Missense 2/6 -
7-140481411-C-G BRAF c.1397G>C p.Gly466Ala Missense 11/18 -
7-140481411-C-T BRAF c.1397G>A p.Gly466Glu Missense 11/18 -
12-25398282-C-T KRAS c.37G>A p.Gly13Ser Missense 2/6 -
12-25398282-C-G KRAS c.37G>C p.Gly13Arg Missense 2/6 -
4-1806099-A-G FGFR3 c.1118A>G p.Tyr373Cys Missense 9/18 -
19-17954215-G-T JAK3 c.394C>A p.Pro132Thr Missense 4/24 -
10-43609950-C-G RET c.1902C>G p.Cys634Trp Missense 11/20 -
7-55241708-G-A EGFR c.2156G>A p.Gly719Asp Missense 18/28 -
3-41266101-C-A CTNNB1 c.98C>A p.Ser33Tyr Missense 3/16 -
3-178938860-A-C PIK3CA c.2102A>C p.His701Pro Missense 14/21 -
3-41266101-C-T CTNNB1 c.98C>T p.Ser33Phe Missense 3/16 -
3-41266101-C-G CTNNB1 c.98C>G p.Ser33Cys Missense 3/16 -
7-140481411-C-A BRAF c.1397G>T p.Gly466Val Missense 11/18 -
7-140481418-C-G BRAF c.1390G>C p.Gly464Arg Missense 11/18 -
7-140453149-C-G BRAF c.1786G>C p.Gly596Arg Missense 15/18 -
7-140453132-T-A BRAF c.1803A>T p.Lys601Asn Missense 15/18 -
17-37880997-G-A ERBB2 c.2326G>A p.Gly776Ser Missense 20/27 -
3-41266064-G-A CTNNB1 c.61G>A p.Ala21Thr Missense 3/16 -
7-116411990-C-T MET c.2975C>T p.Thr992Ile Missense 14/21 -
3-41266124-A-C CTNNB1 c.121A>C p.Thr41Pro Missense 3/16 -
3-41266124-A-T CTNNB1 c.121A>T p.Thr41Ser Missense 3/16 -
12-25398262-C-A KRAS c.57G>T p.Leu19Phe Missense 2/6 -
4-55595519-C-T KIT c.2009C>T p.Thr670Ile Missense 14/21 -
3-41266113-C-A CTNNB1 c.110C>A p.Ser37Tyr Missense 3/16 -
17-37880261-G-C ERBB2 c.2305G>C p.Asp769His Missense 19/27 -
7-55242478-G-C EGFR c.2248G>C p.Ala750Pro Missense 19/28 -
7-55259514-C-A EGFR c.2572C>A p.Leu858Met Missense 21/28 -
19-1220488-A-T STK11 c.581A>T p.Asp194Val Missense 4/10 -
7-55242481-AACA-A EGFR c.2251_2253delACA p.Thr751delThr InFrameDeletion 19/28 -
3-37067240-T-A MLH1 c.1151T>A p.Val384Asp Missense 12/19 -
13-28608341-T-C FLT3 c.1715A>G p.Tyr572Cys Missense 14/24 -
7-140453121-CT-TT BRAF c.1813_1814delAGinsTT p.Ser605Phe Missense 15/18 -
4-55593609-G-A KIT c.1675G>A p.Val559Ile Missense 11/21 -
7-140453137-C-T BRAF c.1798G>A p.Val600Met Missense 15/18 -
5-149433646-A-G CSF1R c.2905T>C p.Tyr969His Missense 22/22 -
7-55242418-C-T EGFR c.2188C>T p.Leu730Phe Missense 19/28 -
4-55593603-T-G KIT c.1669T>G p.Trp557Gly Missense 11/21 -
7-55242511-G-T EGFR c.2281G>T p.Asp761Tyr Missense 19/28 -
4-55593603-T-A KIT c.1669T>A p.Trp557Arg Missense 11/21 -
9-21971108-C-A CDKN2A c.250G>T p.Asp84Tyr Missense 2/3 -
10-89711900-G-A PTEN c.518G>A p.Arg173His Missense 6/9 -
7-140453151-A-G BRAF c.1784T>C p.Phe595Ser Missense 15/18 -
7-140453145-A-C BRAF c.1790T>G p.Leu597Arg Missense 15/18 -
4-1806089-G-T FGFR3 c.1108G>T p.Gly370Cys Missense 9/18 -
7-140481402-C-A BRAF c.1406G>T p.Gly469Val Missense 11/18 -
7-140481402-C-T BRAF c.1406G>A p.Gly469Glu Missense 11/18 -
15-66727455-G-T MAP2K1 c.171G>T p.Lys57Asn Missense 2/11 -
7-55242430-G-A EGFR c.2200G>A p.Glu734Lys Missense 19/28 -
7-140453139-G-A BRAF c.1796C>T p.Thr599Ile Missense 15/18 -
12-25398262-C-G KRAS c.57G>C p.Leu19Phe Missense 2/6 -
5-149453044-A-G CSF1R c.902T>C p.Leu301Ser Missense 7/22 -
7-55242511-G-A EGFR c.2281G>A p.Asp761Asn Missense 19/28 -
4-55152104-G-T PDGFRA c.2536G>T p.Asp846Tyr Missense 18/23 -
17-37880219-TT-CC ERBB2 c.2263_2264delTTinsCC p.Leu755Pro Missense 19/27 -
3-178936092-A-G PIK3CA c.1634A>G p.Glu545Gly Missense 10/21 -
3-178936092-A-C PIK3CA c.1634A>C p.Glu545Ala Missense 10/21 -
15-66727455-G-C MAP2K1 c.171G>C p.Lys57Asn Missense 2/11 -
7-55249131-G-A EGFR c.2429G>A p.Gly810Asp Missense 20/28 -
3-41266113-C-T CTNNB1 c.110C>T p.Ser37Phe Missense 3/16 -
4-55593603-T-C KIT c.1669T>C p.Trp557Arg Missense 11/21 -
3-178921553-T-A PIK3CA c.1035T>A p.Asn345Lys Missense 5/21 -
10-43615624-AAGA-A RET c.2703_2705delAGA p.Glu902delGlu InFrameDeletion 15/20 -
19-17945696-C-T JAK3 c.2164G>A p.Val722Ile Missense 16/24 -
13-28592640-A-C FLT3 c.2505T>G p.Asp835Glu Missense 20/24 -
12-25380276-T-G KRAS c.182A>C p.Gln61Pro Missense 3/6 -
8-38282209-G-T FGFR1 c.754C>A p.Pro252Thr Missense 7/18 -
9-21971111-G-A CDKN2A c.247C>T p.His83Tyr Missense 2/3 -
4-1807889-A-C FGFR3 c.1948A>C p.Lys650Gln Missense 14/18 -
13-28592640-A-T FLT3 c.2505T>A p.Asp835Glu Missense 20/24 -
19-40742220-T-C AKT2 c.904A>G p.Ser302Gly Missense 10/14 -
9-133738306-G-A ABL1 c.763G>A p.Glu255Lys Missense 4/11 -
10-43609945-GCTG-G RET c.1897_1899delCTG p.Leu633delLeu InFrameDeletion 11/20 -
7-55249130-G-A EGFR c.2428G>A p.Gly810Ser Missense 20/28 -
4-55599348-T-C KIT c.2474T>C p.Val825Ala Missense 17/21 -
4-55593610-T-C KIT c.1676T>C p.Val559Ala Missense 11/21 -
7-140481412-C-G BRAF c.1396G>C p.Gly466Arg Missense 11/18 -
7-140481412-C-T BRAF c.1396G>A p.Gly466Arg Missense 11/18 -
4-55593610-T-A KIT c.1676T>A p.Val559Asp Missense 11/21 -
7-140453150-A-C BRAF c.1785T>G p.Phe595Leu Missense 15/18 -
3-178936082-G-C PIK3CA c.1624G>C p.Glu542Gln Missense 10/21 -
4-55561764-G-A KIT c.154G>A p.Asp52Asn Missense 2/21 -
10-43609940-A-G RET c.1892A>G p.Asp631Gly Missense 11/20 -
7-140481403-C-G BRAF c.1405G>C p.Gly469Arg Missense 11/18 -
7-140481403-C-T BRAF c.1405G>A p.Gly469Arg Missense 11/18 -
3-10183785-T-C VHL c.254T>C p.Leu85Pro Missense 1/3 -
4-55594258-T-C KIT c.1961T>C p.Val654Ala Missense 13/21 -
9-80409488-T-G GNAQ c.626A>C p.Gln209Pro Missense 5/7 -
4-1808331-G-T FGFR3 c.2089G>T p.Gly697Cys Missense 16/18 -
7-140453145-AG-TC BRAF c.1789_1790delCTinsTC p.Leu597Ser Missense 15/18 -
4-55152101-GCAT-G PDGFRA c.2533_2535delCAT p.His845delHis InFrameDeletion 18/23 -
20-57484596-A-T GNAS c.680A>T p.Gln227Leu Missense 9/13 -
7-140453136-A-G BRAF c.1799T>C p.Val600Ala Missense 15/18 -
15-66727483-G-A MAP2K1 c.199G>A p.Asp67Asn Missense 2/11 -
4-55599320-G-C KIT c.2446G>C p.Asp816His Missense 17/21 -
17-37880220-T-C ERBB2 c.2264T>C p.Leu755Ser Missense 19/27 -
9-21971036-C-A CDKN2A c.322G>T p.Asp108Tyr Missense 2/3 -
3-10191480-T-A VHL c.473T>A p.Leu158Gln Missense 3/3 -
3-178936091-G-C PIK3CA c.1633G>C p.Glu545Gln Missense 10/21 -
4-55599320-G-T KIT c.2446G>T p.Asp816Tyr Missense 17/21 -
3-41266137-C-G CTNNB1 c.134C>G p.Ser45Cys Missense 3/16 -
8-38285938-G-A FGFR1 c.374C>T p.Ser125Leu Missense 4/18 -
4-1806092-A-T FGFR3 c.1111A>T p.Ser371Cys Missense 9/18 -
7-140453153-A-C BRAF c.1782T>G p.Asp594Glu Missense 15/18 -
10-43609949-G-A RET c.1901G>A p.Cys634Tyr Missense 11/20 -
3-41266136-T-C CTNNB1 c.133T>C p.Ser45Pro Missense 3/16 -
3-41266136-T-G CTNNB1 c.133T>G p.Ser45Ala Missense 3/16 -
15-66727451-A-C MAP2K1 c.167A>C p.Gln56Pro Missense 2/11 -
3-41266104-G-A CTNNB1 c.101G>A p.Gly34Glu Missense 3/16 -
13-28592640-TATC-T FLT3 c.2503_2505delGAT p.Asp835delAsp InFrameDeletion 20/24 -
7-140453193-T-C BRAF c.1742A>G p.Asn581Ser Missense 15/18 -
4-55593689-C-T KIT c.1755C>T p.Pro585Pro Synonymous 11/21 -
9-21971017-G-A CDKN2A c.341C>T p.Pro114Leu Missense 2/3 -
3-41266104-G-T CTNNB1 c.101G>T p.Gly34Val Missense 3/16 -
10-43613840-G-T RET c.2304G>T p.Glu768Asp Missense 13/20 -
10-89711899-C-T PTEN c.517C>T p.Arg173Cys Missense 6/9 -
13-28592641-T-A FLT3 c.2504A>T p.Asp835Val Missense 20/24 -
10-43615568-GC-TT RET c.2647_2648delGCinsTT p.Ala883Phe Missense 15/20 -
10-43609948-T-C RET c.1900T>C p.Cys634Arg Missense 11/20 -
12-25398281-C-A KRAS c.38G>T p.Gly13Val Missense 2/6 -
3-178936094-C-A PIK3CA c.1636C>A p.Gln546Lys Missense 10/21 -
3-41266097-G-A CTNNB1 c.94G>A p.Asp32Asn Missense 3/16 -
3-41266097-GGAC-G CTNNB1 c.94_96delGAC p.Asp32delAsp InFrameDeletion 3/16 -
3-41266097-G-C CTNNB1 c.94G>C p.Asp32His Missense 3/16 -
3-10183797-T-A VHL c.266T>A p.Leu89His Missense 1/3 -
4-1803564-C-T FGFR3 c.742C>T p.Arg248Cys Missense 7/18 -
10-89692905-G-A PTEN c.389G>A p.Arg130Gln Missense 5/9 -
10-89692904-C-G PTEN c.388C>G p.Arg130Gly Missense 5/9 -
3-10191506-C-T VHL c.499C>T p.Arg167Trp Missense 3/3 -
3-41266068-T-C CTNNB1 c.65T>C p.Val22Ala Missense 3/16 -
3-10183772-C-T VHL c.241C>T p.Pro81Ser Missense 1/3 -
7-55242464-A-G EGFR c.2234A>G p.Lys745Arg Missense 19/28 -
7-55242428-C-T EGFR c.2198C>T p.Pro733Leu Missense 19/28 -
12-25380277-G-C KRAS c.181C>G p.Gln61Glu Missense 3/6 -
12-25380277-G-T KRAS c.181C>A p.Gln61Lys Missense 3/6 -
4-55152092-AGAC-A PDGFRA c.2524_2526delGAC p.Asp842delAsp InFrameDeletion 18/23 -
3-178952084-C-T PIK3CA c.3139C>T p.His1047Tyr Missense 21/21 -
7-55242505-AATC-A EGFR c.2275_2277delATC p.Ile759delIle InFrameDeletion 19/28 -
3-178952007-A-G PIK3CA c.3062A>G p.Tyr1021Cys Missense 21/21 -
20-57484421-G-A GNAS c.602G>A p.Arg201His Missense 8/13 -
4-55152098-CATG-C PDGFRA c.2530_2532delATG p.Met844delMet InFrameDeletion 18/23 -
10-43613840-G-C RET c.2304G>C p.Glu768Asp Missense 13/20 -
3-41266137-C-A CTNNB1 c.134C>A p.Ser45Tyr Missense 3/16 -
12-25380283-C-T KRAS c.175G>A p.Ala59Thr Missense 3/6 -
7-140453175-T-G BRAF c.1760A>C p.Asp587Ala Missense 15/18 -
4-55593606-GAAG-G KIT c.1672_1674delAAG p.Lys558delLys InFrameDeletion 11/21 -
3-178936093-G-T PIK3CA c.1635G>T p.Glu545Asp Missense 10/21 -
4-55602694-G-A KIT c.2515G>A p.Glu839Lys Missense 18/21 -
15-66729163-C-T MAP2K1 c.371C>T p.Pro124Leu Missense 3/11 -
12-25398255-G-T KRAS c.64C>A p.Gln22Lys Missense 2/6 -
7-55242433-G-A EGFR c.2203G>A p.Gly735Ser Missense 19/28 -
19-1221319-C-T STK11 c.842C>T p.Pro281Leu Missense 6/10 -
12-58145430-C-T CDK4 c.71G>A p.Arg24His Missense 2/8 -
10-43609102-CTGC-C RET c.1858_1860delTGC p.Cys620delCys InFrameDeletion 10/20 -
7-140453174-G-T BRAF c.1761C>A p.Asp587Glu Missense 15/18 -
7-55242476-GAAG-G EGFR c.2246_2248delAAG p.Glu749delGlu InFrameDeletion 19/28 -
4-55593618-GGAG-G KIT c.1684_1686delGAG p.Glu562delGlu InFrameDeletion 11/21 -
13-49037877-G-T RB1 c.2117G>T p.Cys706Phe Missense 21/27 -
3-178952074-G-A PIK3CA c.3129G>A p.Met1043Ile Missense 21/21 -
3-41266098-A-G CTNNB1 c.95A>G p.Asp32Gly Missense 3/16 -
7-55242485-C-A EGFR c.2255C>A p.Ser752Tyr Missense 19/28 -
4-55141036-T-A PDGFRA c.1682T>A p.Val561Asp Missense 12/23 -
7-55242466-G-A EGFR c.2236G>A p.Glu746Lys Missense 19/28 -
3-41266098-A-T CTNNB1 c.95A>T p.Asp32Val Missense 3/16 -
1-115258730-C-T NRAS c.52G>A p.Ala18Thr Missense 2/7 -
9-133738307-A-T ABL1 c.764A>T p.Glu255Val Missense 4/11 -
4-55594221-A-G KIT c.1924A>G p.Lys642Glu Missense 13/21 -
3-41266097-G-T CTNNB1 c.94G>T p.Asp32Tyr Missense 3/16 -
13-28592642-C-G FLT3 c.2503G>C p.Asp835His Missense 20/24 -
19-40741860-C-T AKT2 c.1112G>A p.Arg371His Missense 11/14 -
3-178952074-G-C PIK3CA c.3129G>C p.Met1043Ile Missense 21/21 -
17-37881000-G-C ERBB2 c.2329G>C p.Val777Leu Missense 20/27 -
3-41266040-G-A CTNNB1 c.37G>A p.Ala13Thr Missense 3/16 -
17-37881000-G-T ERBB2 c.2329G>T p.Val777Leu Missense 20/27 -
7-140453132-ATTT-A BRAF c.1801_1803delAAA p.Lys601delLys InFrameDeletion 15/18 -
3-41266125-C-T CTNNB1 c.122C>T p.Thr41Ile Missense 3/16 -
3-41266103-G-A CTNNB1 c.100G>A p.Gly34Arg Missense 3/16 -
3-41266103-G-C CTNNB1 c.100G>C p.Gly34Arg Missense 3/16 -
7-140453161-T-C BRAF c.1774A>G p.Ile592Val Missense 15/18 -
3-178952090-G-C PIK3CA c.3145G>C p.Gly1049Arg Missense 21/21 -
7-140453154-T-A BRAF c.1781A>T p.Asp594Val Missense 15/18 -
4-55152092-GA-AT PDGFRA c.2524_2525delGAinsAT p.Asp842Ile Missense 18/23 -
3-178952090-G-A PIK3CA c.3145G>A p.Gly1049Ser Missense 21/21 -
4-55593613-T-A KIT c.1679T>A p.Val560Asp Missense 11/21 -
3-41266113-C-G CTNNB1 c.110C>G p.Ser37Cys Missense 3/16 -
19-17948009-G-A JAK3 c.1715C>T p.Ala572Val Missense 13/24 -
4-55593613-T-G KIT c.1679T>G p.Val560Gly Missense 11/21 -
7-55242487-C-T EGFR c.2257C>T p.Pro753Ser Missense 19/28 -
19-1220494-G-T STK11 c.587G>T p.Gly196Val Missense 4/10 -
19-1220487-G-A STK11 c.580G>A p.Asp194Asn Missense 4/10 -
4-55152104-TGAT-T PDGFRA c.2536_2538delGAT p.Asp846delAsp InFrameDeletion 18/23 -
4-55152092-G-T PDGFRA c.2524G>T p.Asp842Tyr Missense 18/23 -
7-140453153-A-T BRAF c.1782T>A p.Asp594Glu Missense 15/18 -
7-55242484-ATCT-A EGFR c.2254_2256delTCT p.Ser752delSer InFrameDeletion 19/28 -
7-55249020-A-G EGFR c.2318A>G p.His773Arg Missense 20/28 -
3-41266116-GGTG-G CTNNB1 c.113_115delGTG p.Gly38delGly InFrameDeletion 3/16 -
15-66729153-T-A MAP2K1 c.361T>A p.Cys121Ser Missense 3/11 -
4-55599340-T-A KIT c.2466T>A p.Asn822Lys Missense 17/21 -
4-55599340-T-G KIT c.2466T>G p.Asn822Lys Missense 17/21 -
4-55593610-T-G KIT c.1676T>G p.Val559Gly Missense 11/21 -
7-140481417-C-A BRAF c.1391G>T p.Gly464Val Missense 11/18 -
7-140481417-C-T BRAF c.1391G>A p.Gly464Glu Missense 11/18 -
19-1220502-G-A STK11 c.595G>A p.Glu199Lys Missense 4/10 -
3-178952074-G-T PIK3CA c.3129G>T p.Met1043Ile Missense 21/21 -
4-55593613-GTTG-G KIT c.1679_1681delTTG p.Val560delVal InFrameDeletion 11/21 -
3-41266098-A-C CTNNB1 c.95A>C p.Asp32Ala Missense 3/16 -
7-140453121-C-T BRAF c.1814G>A p.Ser605Asn Missense 15/18 -
13-28592637-G-C FLT3 c.2508C>G p.Ile836Met Missense 20/24 -
7-140453159-T-C BRAF c.1776A>G p.Ile592Met Missense 15/18 -
13-28592637-TGAT-T FLT3 c.2508_2510delCAT p.Ile836delIle InFrameDeletion 20/24 -
7-140481418-C-T BRAF c.1390G>A p.Gly464Arg Missense 11/18 -
7-140453179-C-T BRAF c.1756G>A p.Glu586Lys Missense 15/18 -
5-149433645-T-A CSF1R c.2906A>T p.Tyr969Phe Missense 22/22 -
5-149433645-T-C CSF1R c.2906A>G p.Tyr969Cys Missense 22/22 -
3-178936074-C-G PIK3CA c.1616C>G p.Pro539Arg Missense 10/21 -
7-140453146-G-C BRAF c.1789C>G p.Leu597Val Missense 15/18 -
7-55242455-T-C EGFR c.2225T>C p.Val742Ala Missense 19/28 -
15-66729154-G-C MAP2K1 c.362G>C p.Cys121Ser Missense 3/11 -
7-140453145-A-T BRAF c.1790T>A p.Leu597Gln Missense 15/18 -
7-140453150-A-T BRAF c.1785T>A p.Phe595Leu Missense 15/18 -
7-140481478-G-A BRAF c.1330C>T p.Arg444Trp Missense 11/18 -