Table 1. BRCA1 and BRCA2 variations used for the NGS validation.
| Patients | Gene a | Type | site | Description b | Expected consequence c | Detectable with Casava | Detectable with NextGene | Detectable with CNVseq |
|---|---|---|---|---|---|---|---|---|
| T1 | BRCA1 | LGR | Del 1–24 | c.1-?_5592+?del | p.? | NA | NA | Yes |
| T2 | BRCA1 | LGR | Dup 5–7 | c.135-?_441+?dup | p.? | NA | NA | Yes |
| T3 | BRCA1 | indel | Ex 11 | c.2612_2613insT | p.Phe872Valfs*31 | Yes | Yes | NA |
| T4 | BRCA1 | LGR | Dup 13 | c.4186-?_4357+?dup | p.? | NA | NA | Yes |
| T5 | BRCA1 | indel | Ex 13 | c.4282ins39 | p.Ser1428* | Yes | Yes | NA |
| T6 | BRCA1 | indel | Ex 18 | c.5077_5080delinsTTCATTCTGC | p.Ala1693_Glu1694delinsPheIleLeuGln | Yes | Yes | NA |
| T7 | BRCA2 | indel | Ex 9 | c.736_755del | p.Phe246Glnfs*2 | Yes | Yes | NA |
| T8 | BRCA2 | indel | Ex 10 | c.1231_1241delinsACAT | p.Ile411Thrfs*17 | Yes | Yes | NA |
| T9 | BRCA2 | SNV | Ex 12 | c.6848C>A | p.Pro2283His | Yes | Yes | NA |
| T10 | BRCA2 | indel | Ex 14 | c.7069_7070del | p.Leu2357Valfs*2 | Yes | Yes | NA |
| T11 | BRCA2 | indel | Ex 23 | c.9097dup | p.Thr3033Asnfs*11 | Yes | Yes | NA |
| T12 | BRCA1 | indel | Ex 11 | c.1175_1214del | p.Leu392Glnfs*5 | Yes | Yes | NA |
| T13 | BRCA1 | indel | Ex 11 | c.3481_3491del | p.Glu1161Phefs*3 | Yes | Yes | NA |
| T14 | BRCA1 | indel | Ex 11 | c.3947_3950delTCTT | p.Phe1316* | Yes | Yes | NA |
| T15 | BRCA1 | indel | Int 20 | c.5277+48_5277+59dup | p.? | No | Yes | NA |
| T16 | BRCA1 | indel | Ex 11 | c.3731_3738del | p.His1244Argfs*8 | Yes | Yes | NA |
| T17 | BRCA2 | indel | Int 8 | c.681+97_681+98delGT | p.? | Yes | Yes | NA |
| T17 | BRCA1 | indel | Int 21 | c.5332+182dup | p.? | Yes | Yes | NA |
| T18 | BRCA1 | indel | Ex 6 | c.282_288dup | p.Thr97Alafs*2 | Yes | Yes | NA |
| T19 | BRCA1 | indel | Ex 11 | c.2709_2710del | p.Cys903* | Yes | Yes | NA |
| T20 | BRCA1 | indel | Ex 11 | c.1016dup | p.Val340Glyfs*6 | Yes | Yes | NA |
| T21 | BRCA1 | indel | Ex 11 | c.3770_3771del | p.Glu1257Glyfs*9 | Yes | Yes | NA |
| T22 | BRCA1 | indel | Ex 11 | c.3541_3556del | p.Val1181Leufs*24 | Yes | Yes | NA |
| T23 | BRCA1 | indel | Ex 14 | c.4391_4393delinsTT | p.Pro1464Leufs*2 | Yes | Yes | NA |
| T24 | BRCA1 | indel | Ex 11 | c.2269del | p.Val757Phefs*8 | Yes | Yes | NA |
| T25 | BRCA1 | indel | Ex 11 | c.3839_3843delinsAGGC | p.Ser1280* | Yes | Yes | NA |
| T26 | BRCA2 | indel | Ex 25 | c.9435_9436del | p.Ser3147Cysfs*2 | Yes | Yes | NA |
| T27 | BRCA2 | indel | Ex 16 | c.7795_7797del | p.Glu2599del | Yes | Yes | NA |
| T28 | BRCA2 | SNV | Ex 10 | c.1395A>C | p.= | Yes | Yes | NA |
| T28 | BRCA2 | indel | Ex 10 | c.1389_1390del | p.Val464Glyfs*3 | Yes | Yes | NA |
| T29 | BRCA2 | indel | Ex 18 | c.8053del | p.Thr2685Hisfs*9 | Yes | Yes | NA |
| T30 | BRCA2 | indel | Ex 10 | c.1796_1800del | p.Ser599* | Yes | Yes | NA |
| T31 | BRCA2 | indel | Ex 11 | c.6408_6414del | p.Asn2137Lysfs*29 | Yes | Yes | NA |
| T32 | BRCA2 | indel | Ex 8 | c.635_636del | p.Arg212Lysfs*2 | Yes | Yes | NA |
| T33 | BRCA2 | indel | Ex 11 | c.6079dup | p.Arg2027Lysfs*22 | Yes | Yes | NA |
| T34 | BRCA2 | indel | Ex 27 | c.9699_9702del | p.Cys3233Trpfs*15 | Yes | Yes | NA |
| T35 | BRCA2 | indel | Ex 9 | c.755_758del | p.Asp252Valfs*24 | Yes | Yes | NA |
| T36 | BRCA2 | indel | Ex 11 | c.5810_5811del | p.Ser1937Trpfs*7 | Yes | Yes | NA |
| T37 | BRCA2 | indel | Ex 22 | c.8773_8780dup | p.Arg2927Serfs*3 | Yes | Yes | NA |
| T38 | BRCA1 | SNV | Int 5 | c.213-1G>A | p.? | Yes | Yes | NA |
| T39 | BRCA1 | SNV | Ex 11 | c.3979C>T | p.Gln1327* | Yes | Yes | NA |
| T40 | BRCA2 | SNV | Int 6 | c.516+2T>C | p.? | Yes | Yes | NA |
| T41 | BRCA2 | SNV | Ex 13 | c.7007G>A | p.Arg2336His | Yes | Yes | NA |
| T42 | BRCA2 | SNV | Ex 12 | c.6848C>A | p.Pro2283His | Yes | Yes | NA |
| T43 | BRCA2 | SNV | Ex 15 | c.7558C>T | p.Arg2520* | Yes | Yes | NA |
| T44 | BRCA2 | SNV | Ex 21 | c.8707G>T | p.Glu2903* | Yes | Yes | NA |
| T45 | BRCA2 | SNV | Ex 3 | c.273C>A | p.Tyr91* | Yes | Yes | NA |
| T46 | BRCA1 | LGR | Del 1–2 | c.-232-?_80+?del | p.? | NA | NA | Yes |
| T47 | BRCA1 | LGR | Del 11–12 | c.671-?_4185+?del | p.? | NA | NA | Yes |
| T48 | BRCA1 | LGR | Del 3 | c.81-?_134+?del | p.? | NA | NA | Yes |
| T49 | BRCA1 | LGR | Del 8–13 | c.442-?_4357+?del | p.? | Yes | Yes | NA |
| T49 | BRCA2 | indel | Ex 11 | c.5272_5274del | p.Asn1758del | Yes | Yes | NA |
| T50 | BRCA1 | LGR | Del 3–16 | c.81-?_4986+?del | p.? | NA | NA | Yes |
| T51 | BRCA1 | LGR | Del 5–24 | c.135-?_5592+?del | p.? | NA | NA | Yes |
| T52 | BRCA1 | LGR | Del 17 | c.4987-?_5074+?del | p.? | NA | NA | Yes |
| T53 | BRCA1 | LGR | Dup 3–8 | c.81-?_547+?dup | p.? | NA | NA | Yes |
| T54 | BRCA1 | LGR | Del 22 | c.5333-?_5406+?del | p.? | NA | NA | Yes |
| T55 | BRCA1 | LGR | Del NBR2-2 | c.-232-?_80+?del | p.? | NA | NA | Yes |
| T56 | BRCA1 | LGR | Del 21 | c.5278-?_5332+?del | p.? | NA | NA | Yes |
| T57 | BRCA1 | LGR | Del 20 | c.5194-?_5277+?del | p.? | NA | NA | Yes |
| T58 | BRCA2 | LGR | Del 12–13 | c.6842-?_7007+?del | p.? | NA | NA | Yes |
| T59 | BRCA2 | indel | Ex 3 | c.156_157insAlud | p.? | Yes | No | No |
Abbreviations: LGR, large genomic rearrangement; NA, not applicable.
a
Nomenclature was numbered on the basis of the transcript NM_007294 for BRCA1 and NM_000059 for BRCA2.
b
Mutation nomenclature according to HGVS recommendations, nucleotide position was numbered with +1 corresponding to the A of the ATG of the translation initiation codon.
c
Expected consequence on the protein level.
d
Corresponding to the Portuguese founder mutation c.156_157insAP003441.3:g.105088_105370.