Table 1 Mechanisms of biallelic loss at the germline locus in BRCA1 and BRCA2 mutation germline mutation-associated tumors

From: BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers

ASCN analysis of locus-specific LOHa

BRCA1 germline mutation

BRCA2 germline mutation

 

TCGA (n = 55)

Local (n = 38)

TCGA (n = 45)

Local (n = 22)

LOH with deletion

9

16%

8

21%

8

18%

6

27%

Copy neutral LOH

23

42%

13

34%

15

34%

5

23%

LOH in gain

20

36%

11

29%

7

16%

4

18%

Absent locus-specific LOH

2

4%

6

16%

13

29%

8

36%

Absent LOH + somatic mutationb

1

2%

0

0%

1

2%

0

0%

  1. aAllele-specific copy number analysis (ASCN) at BRCA1 or BRCA2 genomic locus. Categories of allele-specific copy number loss are defined as per the output of the Sequenza program: loss of heterozygosity (LOH) with deletion refers to copy number state of one with one mutant allele; copy neutral LOH refers to copy number state of two with two mutant alleles; LOH in gain refers to copy number state of ≥3 with all mutant alleles; absent locus-specific LOH refers to copy number state of ≥2 and at least one wildtype allele
  2. bIdentification of a somatic mutation in the corresponding gene in the tumor
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