Table 1 Rare cancer CNVs at known cancer-predisposing genes

APC

Adenomatous polyposis coli; Turcot syndrome

Hodgson et al. [36], Su et al. [37], Aretz et al. [38] and

Charames et al. [39]

BMPR1A

Juvenile polyposis

Delnatte et al. [40]

BRCA1

Hereditary breast/ovarian cancer

Petrij-Bosch et al. [41] and Montagna et al. [42]

BRCA2

Hereditary breast/ovarian cancer

Casilli et al. [43]

CDKN2A-p14ARF

Familial malignant melanoma

Lesueur et al. [44]

CDKN2A-p16(INK4a)

Familial malignant melanoma

Lesueur et al. [44]

CHEK2

Familial breast cancer

Cybulski et al. [45, 46]

FANCA

Fanconi anemia A

Levran et al. [47]

MADH4

Juvenile polyposis

van Hattem et al. [48]

MEN1

Multiple endocrine neoplasia type 1

Kishi et al. [49]

MLH1

Hereditary non-polyposis colorectal cancer, Turcot syndrome

Nystrom-Lahti et al. [50] Chan et al. [51]

MSH2

Hereditary non-polyposis colorectal cancer

Stella et al. [52]

MSH6

Hereditary non-polyposis colorectal cancer

Plaschke et al. [53]

NF1

Neurofibromatosis type 1

Riva et al. [54], Bausch et al. [55]

NF2

Neurofibromatosis type 2

Tsilchorozidou et al. [56]

PRKAR1A

Carney complex

Horvath et al. [57]

PTCH

Nevoid basal cell carcinoma syndrome

Shimkets et al. [58]

RB1

Familial retinoblastoma

Bremner et al. [59]

SDHB

Familial paraganglioma

Cascon et al. [60]

SDHC

Familial paraganglioma

Baysal et al. [61]

SDHD

Familial paraganglioma

McWhinney et al. [62]

SMARCB1

Rhabdoid predisposition syndrome

Swensen et al. [63]

STK11

Peutz-Jeghers syndrome

Le Meur et al. [64]

TP53

Li-Fraumeni syndrome

Bougeard et al. [65, 66]

TSC1

Tuberous sclerosis 1

Kozlowski et al. [67]

TSC2

Tuberous sclerosis 2

Kozlowski et al. [67]

VHL

von Hippel-Lindau syndrome

Richards et al. [68]

WT1

Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor

Huff et al. [69]