CancerNext-ExpandedTM is a next generation sequencing panel that simultaneously analyzes 67 genes associated with increased risks for brain, breast, colon, ovarian, pancreatic, prostate, renal, uterine, and many other cancers.
CancerNext-ExpandedTM is a next generation sequencing panel that simultaneously analyzes 67 genes associated with increased risks for brain, breast, colon, ovarian, pancreatic, prostate, renal, uterine, and many other cancers.
Ambry utilizes next generation sequencing (NGS) to offer CancerNext-Expanded, its comprehensive hereditary pan-cancer panel. Genes on this panel include: AIP, ALK, APC, ATM, BAP1, BARD1, BLM, BRCA1, BRCA2, BRIP1, BMPR1A, CDH1, CDK4, CDKN1B, CDKN2A, CHEK2, DICER1, EPCAM, FANCC, FH, FLCN, GALNT12, GREM1, HOXB13, MAX, MEN1, MET, MITF, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, NF2, PALB2, PHOX2B, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TMEM127, TP53, TSC1, TSC2, VHL, XRCC2. Full gene sequencing is performed for 65 of the genes (excluding EPCAM and GREM1). For MITF, only the status of the c.952G>A (p.E318K) alteration is analyzed and reported. Gross deletion/duplication analysis is performed for 66 genes (excluding MITF). Specific Site Analysis is available for individual gene mutations identified in a family.
Brain tumors are the 16th most common cancer diagnosed in men and women. Fewer than 1% of men and women in the U.S. will be diagnosed with a brain tumor/cancer at some point during their lives.1 The National Cancer Institute (NCI) estimates that approximately 23,700 new cases of brain and other nervous system tumors/cancer will be diagnosed in the U.S. in 2016.2 The median age at diagnosis is age 58, although 43.6% are diagnosed under age 54.2 The majority of brain tumors are sporadic, with some being hereditary and developing due to an inherited genetic mutation. Hereditary brain tumors may be diagnosed at younger ages (especially in childhood).
Breast cancer is the most common cancer in women in developed countries, affecting about 1 in 8 (12.5%) women in their lifetime.1 The National Cancer Institute (NCI) estimates that approximately 231,840 new cases of female breast cancer and 2,350 new cases of male breast cancer will be diagnosed in the U.S. in 2015.2 The majority of breast cancers are sporadic, but 5-10% are due to inherited causes. Hereditary breast cancer tends to occur earlier in life than non-inherited sporadic cases, and is more likely to occur in both breasts. The highly penetrant genes, BRCA1 and BRCA2, appear to be responsible for around half of hereditary breast cancer.3-5 However, additional genes have been discovered that are associated with increased breast cancer risk as well.3-7 Mutations in the genes included in CancerNext-Expanded can confer an estimated 20–87% lifetime risk for breast cancer. Some of these genes have also been associated with increased risks for other cancers, such as pancreatic cancer with PALB2, ovarian cancer with BRCA1, BRCA2, RAD51C (and others), and sarcoma with TP53.8-12
Colorectal cancer (CRC) affects about 1 in 20 (5%) men and women in their lifetime.1 The NCI estimates that approximately 132,700 new cases will be diagnosed and 49,700 CRC deaths will occur in the U.S. in 2015.2 The majority of CRC is sporadic, but approximately 30% are familial, a subset of which have a strong genetic cause. Lynch syndrome is the most common form of hereditary CRC, but several other genes are associated with increased CRC risk as well.13
Kidney cancer affects about 1 in 60 (1.6%) of men and women in the U.S. in their lifetime and it is the seventh and eighth most common cancer in men and women, respectively.1 Renal cell carcinoma (RCC) is a complex disease with a diverse spectrum of tumor subtypes, including clear cell or conventional (70-80%), papillary type 1 and type 2 (10-15%), chromophobe (3-5%), and collecting duct (1%).14 3-5% of RCC cases are hereditary15-17 and occur as a result of an inherited mutation in one or more genes. Unlike sporadic RCC cases, hereditary RCC is often characterized by earlier disease onset and/or multifocal or bilateral tumors.14
Ovarian cancer is the fifth most common cancer among women in developed countries, affecting approximately 1 in 71 (1.4%) women in their lifetime.1 The NCI estimates that approximately 21,290 new cases of ovarian cancer will be diagnosed and 14,180 ovarian cancer deaths will occur in the U.S. in 2015.2 It is the leading cause of death from gynecologic malignancy, usually characterized by advanced presentation with regional dissemination in the peritoneal cavity. Epithelial ovarian cancer is the most common form, and up to 25% of epithelial cases may be due to inherited gene mutations.18,19 BRCA1 and BRCA2 are the most common causes of hereditary ovarian cancer, but several other genes are associated with increased ovarian cancer risk as well.11,18,20,21
Pancreatic cancer affects about 1 in 65 (1.5%) of men and women in their lifetime.1 The National Cancer Institute (NCI) estimates that approximately 48,960 new cases of pancreatic cancer will be diagnosed in the U.S. in 2015.2 Approximately 95% of pancreatic cancers are pancreatic adenocarcinomas of the exocrine gland (which produces enzymes for food digestion). Neuroendocrine/islet cell tumors of the endocrine gland (a gland that produces insulin and regulates blood sugar) make up the other 5% of pancreatic cancer subtypes. While the majority of pancreatic cancers are sporadic, approximately 5-10% of pancreatic cancer cases are familial, often occurring in families with multiple affected individuals.23 Multiple genes are associated with increased pancreatic cancer susceptibility.
Paragangliomas (PGLs) are often benign, neuroendocrine tumors of the autonomic nervous system originating from the external ganglia. Pheochromocytomas (PCCs) are PGLs that are confined to the adrenal medulla. PGLs are further subdivided into sympathetic and parasympathetic tumors, depending upon their site of origin. Sympathetic PGLs commonly hypersecrete catecholamines and are typically located in the chest, abdomen and pelvis. Parasympathetic PGLs are primarily non-secretory and occur along the nerves in the head, the neck, and the upper mediastinum (termed head and neck PGLs or HNPGLs).24,25 The prevalence of PGLs in the U.S. is 1 in 2,500 to 1 in 6,500, although this is likely an underestimate. The average age of diagnosis is between 40-50 years.25,26 Approximately 75% of PGL/PCCs are benign; however, morbidity and mortality are associated with high levels of circulating catecholamines, which can lead to hypertension and stroke.24,26 Published population studies have found that at least 10-30% individuals with PGL/PCCs have an inherited germline mutation in one of the known susceptibility genes.24,27-29
Prostate cancer is the second most common cancer in men in the United States, after skin cancer.1 The National Cancer Institute (NCI) estimates that approximately 180,890 new cases of prostate cancer will be diagnosed in the U.S. in 2016.2 The majority of prostate cancer is sporadic and diagnosed over the age of 65. Some prostate cancer may be hereditary and develop due to an inherited genetic mutation. Hereditary prostate cancer may be diagnosed at younger ages and may also be more aggressive. For example, BRCA1 and BRCA2 gene mutations have been shown to be associated with more aggressive prostate cancer, including a higher likelihood of nodal involvement and distant metastasis.30
Uterine cancer affects about 1 in 38 (2.6%) women in their lifetime.1 The NCI estimates that approximately 54,870 new cases of uterine cancer will be diagnosed and 10,170 uterine cancer deaths will occur in the U.S. in 2015.2 Increased risk for uterine cancer has been identified in a number of hereditary cancer syndromes, including Lynch syndrome and Cowden syndrome.
CancerNext-Expanded is an NGS cancer panel that simultaneously analyzes 67 genes associated with an increased risk for several cancers. While mutations in each gene on this panel may be individually rare, they collectively account for a significant amount of hereditary cancer susceptibility. This panel may be appropriate in a number of scenarios, particularly if the family history shares features of several different hereditary cancer syndromes with multiple cancer types.
The following genes are included in CancerNext and CancerNext-Expanded:
APC germline mutations are the primary cause of familial adenomatous polyposis (FAP) and attenuated familial adenomatous polyposis (AFAP). FAP and AFAP are autosomal dominant colon cancer predisposition syndromes characterized by hundreds to thousands of adenomatous polyps in the internal lining of the colon and the rectum. They affect 1 in 8,000 to 1 in 10,000 individuals, and account for about 1% of all colorectal cancers.31 In individuals affected with classic FAP, colonic polyps generally begin developing at an average age of 16 years.32 In these families, colon cancer is inevitable without surgical intervention like colectomy, and the mean age of colon cancer diagnosis in untreated individuals is 35-40 years.33 Individuals with FAP or AFAP may also have increased risks to develop duodenal cancer, pancreatic cancer, papillary thyroid cancer, hepatoblastoma in childhood, and medulloblastoma. Some individuals may also have non-malignant features such as osteomas, congenital hypertrophy of the retinal pigment epithelium (CHRPE), and/or desmoid tumors.31
ATM is a gene associated with an autosomal recessive condition called ataxia-telangiectasia (AT). AT is characterized by progressive cerebellar ataxia with onset between ages 1 and 4, telangiectasia of the conjunctivae, oculomotor apraxia, immune defects, and a predisposition to malignancy, particularly leukemia and lymphoma. Women who carry ATM mutations also have an estimated 2-4 fold increased risk for breast cancer.34 Cancer risk estimates for male ATM mutation carriers are not currently available. Recent studies have also reported ATM germline mutations in individuals with familial pancreatic cancer. In one of these studies, ATM mutations were identified in 4/87 (4.6%) families with more than three affected members.35
BRCA1 and BRCA2 are tumor suppressor genes inherited in an autosomal dominant pattern. Mutations in these two highly penetrant genes increase the chance for cancer of the breast, ovaries (including primary peritoneal and fallopian tube), pancreas, and prostate. Studies suggest female BRCA1 mutation carriers have a 57-87% lifetime risk to develop breast cancer and a 39-40% lifetime risk to develop ovarian cancer by age 70.8-10,36-38 Male BRCA1 mutation carriers have a cumulative breast cancer lifetime risk of about 1.2% by age 70.39,40 Similar studies suggest female BRCA2 mutation carriers have a 45-84% lifetime risk to develop breast cancer and an 11-18% risk to develop ovarian cancer by age 70.8-10,41,42 Male BRCA2 mutation carriers have up a 15% lifetime prostate cancer risk and a cumulative lifetime breast cancer risk of 6.8% by ages 65 and 70 respectively.39,40,42,43 BRCA1/2 mutation carriers may also be at an increased risk for melanoma, pancreatic cancer, and potentially other cancers.44 BRCA2 is also known as FANCD1. Individuals who inherit a BRCA2/FANCD1 mutation from each parent may have a rare autosomal recessive condition called Fanconi anemia type D1 (FA-D1), which affects multiple body systems.
BARD1, BRIP1, MRE11A, NBN, RAD50, RAD51C, and RAD51D are genes involved in the Fanconi anemia (FA)-BRCA pathway, critical for DNA repair by homologous recombination, and interact in vivo with BRCA1 and/or BRCA2.4,20,45 Mutations in these genes are associated with an increased risk for female breast cancer.45-47 The ovarian cancer risk associated with mutations in BRIP1, RAD51C, and RAD51D has been estimated to be up to 9%, 5-9% and 10-12%, respectively.11,21,47-49 It has been suggested that BARD1 is associated with an increased risk for ovarian cancer, and mutations in MRE11A, NBN, and RAD50 have also been reported in at least one identified case of ovarian cancer to date.18,50 BRIP1, NBN, and RAD51C are each associated with a rare autosomal recessive disorder that affects multiple body systems.
BMPR1A and SMAD4 are genes implicated in juvenile polyposis syndrome (JPS), together accounting for 45-60% of JPS. JPS is an autosomal dominant disorder that predisposes to the development of polyps in the gastrointestinal tract.51 Malignant transformation can occur; risk of gastrointestinal cancer ranges from 40-50%. Juvenile polyposis of infancy, which is rare, involves the entire digestive tract and has the poorest prognosis.52 Most patients develop symptoms by age 20, though some are not diagnosed until the third decade of life. Common symptoms include gastrointestinal bleeding, anemia, diarrhea, and abdominal pain. Early detection of JPS allows for better treatment of polyps and surveillance for those at risk. SMAD4 mutations may cause a combined syndrome of hereditary hemorrhagic telangiectasia (HHT) with JPS, as reported in 15-20% of JPS patients with SMAD4 mutations.53
CHEK2 is a gene that receives signals from damaged DNA, transmitted via ATM. CHEK2 interacts in vivo with BRCA1, BRCA2, and TP53, which have all been implicated in cellular processes responsible for the maintenance of genomic stability. Multiple studies indicate that mutations in CHEK2 confer an increased risk of developing many types of cancer including breast, colon, and other cancers. Mutations are more likely to be found among women with bilateral versus unilateral breast cancers. A female CHEK2 mutation carrier has approximately a two-fold increase in lifetime breast cancer risk, and has a 1% risk per year of developing a second breast primary cancer. Lifetime risks for other associated cancers are unknown. An increased risk for ovarian cancer has also been suggested.18,54-56
CDH1 germline mutations are associated with hereditary diffuse gastric cancer (HDGC) and lobular breast cancer in women. In one published study, the estimated cumulative risk of gastric cancer for CDH1 mutation carriers by age 80 years was 67% for men and 83% for women.57 Patients with HDGC typically present with diffuse-type gastric cancer, with signet ring cells diffusely infiltrating the wall of the stomach and, at advanced stages, linitis plastica. An elevated risk of lobular breast cancer in women is also associated with HDGC, with an estimated lifetime breast cancer risk of 39-52%.58
CDK4 is one of the genes associated with cutaneous malignant melanoma (CMM) syndrome. Individuals with CDK4 mutations demonstrate a higher frequency of atypical nevi, an earlier age of melanoma diagnosis (mean age 32-39 years), and an increased likelihood for multiple primary melanomas, as compared to individuals without CDK4 mutations.59,60 It is estimated that CDK4 mutation carriers have up to a 74% lifetime risk for malignant melanoma by age 50.59
CDKN2A encodes two distinct proteins, p16 and p14ARF, which are both involved in cell cycle regulation. Germline p16/CDKN2A mutations are associated with familial atypical multiple mole melanoma (FAMMM) syndrome. FAMMM is an autosomal dominant disorder characterized by an increased risk for atypical mole malignant melanoma, often associated with dysplastic or atypical nevi. CDKN2A mutation carriers have an approximate 28-67% lifetime risk of developing melanoma, with penetrance estimates varying widely based on study design and geographic region.61-63 Individuals carrying CDKN2A mutations also have an approximate 17-25% lifetime risk for pancreatic cancer; however, recent reports suggest this risk may be as high as 58% and elevated further in smokers.64-66 Rare mutations that affect the p14ARF mutations have also been reported to predispose to melanoma and possibly pancreatic cancer.65,67,68
GREM1 A large duplication upstream of GREM1 has been identified families of Ashkenazi Jewish descent with hereditary mixed polyposis. To date, only this founder mutation has been reported, but the possibility of GREM1 mutations in individuals of other ethnicities has not been excluded.69 Manifestations of the GREM1 duplication appear to be limited to the intestinal tract, and include mixed morphology colon polyps and cancer; however, lifetime risk estimates for mutation carriers are not currently available.69,70
MLH1, MSH2, MSH6, PMS2, and EPCAM germline mutations are associated with Lynch syndrome (previously called hereditary non-polyposis colorectal cancer, HNPCC). Lynch syndrome is an autosomal dominant condition estimated to cause 2-5% of all colorectal cancer. It is associated with a significantly increased risk for colorectal cancer (up to 82% lifetime risk), uterine/endometrial cancer (25-60% lifetime risk in women), stomach cancer (6-13% lifetime risk), and ovarian cancer (4-12% lifetime risk in women). Risk for cancer of the small bowel, hepatobiliary tract, upper urinary tract (including transitional cell carcinoma of the renal pelvis), brain, and sebaceous glands may also be elevated.71-75
MUTYH germline mutations are known to cause MUTYH-associated polyposis (MAP), an autosomal recessive condition predisposing to gastrointestinal polyposis and colorectal cancer. Individuals that carry two MUTYH mutations on different chromosomes (in trans) have an estimated lifetime colorectal cancer risk of up to 80%.76 In addition, some studies suggest that MUTYH mutations confer an increased risk to develop female breast cancer; this is estimated to be a 1.5-fold lifetime increased risk within the North African Jewish population. MUTYH mutations in the carrier state may also increase lifetime risks for cancers of the duodenum, stomach, and endometrium;77-79 however, these data are limited and risks may vary between populations. Two common mutations in the Caucasian population, p.Y179C and p.G396D (originally designated as p.Y165C and p.G382D), account for the majority of pathogenic MUTYH alterations reported to date. Breast cancer risk estimates for male MUTYH mutation carriers are not currently available.
NF1 mutations cause neurofibromatosis type 1 (NF1), an autosomal dominant disorder affecting multiple body systems. It is characterized by multiple café-au-lait spots, axillary and inguinal freckling, multiple cutaneous neurofibromas, and Lisch nodules. The most common neoplasms observed in individuals with NF1 include peripheral nerve sheath tumors, gastrointestinal stromal tumors (GIST), central nervous system gliomas, leukemias, paragangliomas (PGLs) and pheochromocytomas (PCCs), and breast cancer. Multiple population-based studies have demonstrated a 3- to 5-fold increase in lifetime breast cancer risk for women with NF1, with the highest risks for those less than 50 years of age. In addition, individuals with NF1 have an estimated lifetime risk for PGLs and PCCs of up to 7%.
PALB2 germline mutations have been associated with an increased lifetime risk for pancreatic cancer, breast cancer, and Fanconi anemia type N (FA-N). Familial pancreatic and/or breast cancer due to PALB2 mutations is inherited in an autosomal dominant pattern, while FA-N is a rare autosomal recessive condition affecting multiple body systems. Females with a PALB2 mutation have a 2- to 4-fold increase in risk for breast cancer.80,81 A 2014 article concluded that in the context of a strong family history, mutations in PALB2 may be associated with up to a 58% risk of female breast cancer. Without a family history, the risk for female breast cancer was estimated to be 33% (the difference attributed to genetic and/or environmental modifiers).82 Studies have identified PALB2 mutations in 1-3% of families with pancreatic cancer; however, the exact lifetime pancreatic cancer risk has not yet been established.83,84 Additionally, recent studies have shown an increased risk for ovarian cancer.18,50
POLD1 and POLE mutations are implicated in an emerging syndrome of colorectal cancer and polyposis, called polymerase proofreading-associated polyposis (PPAP) by some.85 Exact cancer risks for mutation carriers have not yet been determined; however, published studies support POLD1 and POLE mutations as highly penetrant, conferring increased risk for early-onset colorectal cancer and/or multiple adenomas.86,87 Associations between POLD1 and POLE mutations and elevated incidence of extra-intestinal tumors have been suggested, although data is currently limited.
PTEN is a gene associated with Cowden syndrome (CS), PTEN hamartoma tumor syndrome (PHTS), Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, and autism spectrum disorder. CS is a multiple hamartoma syndrome with a high risk of developing tumors of the thyroid, breast, and endometrium. Mucocutaneous lesions, thyroid abnormalities, fibrocystic disease, multiple uterine leiomyomata, and macrocephaly can also be seen. Affected individuals have a lifetime risk of up to 50% for breast cancer, 10% for thyroid cancer, and 5-10% for endometrial cancer. Over 90% of individuals with CS will express some clinical manifestations by their twenties.88,89 Recent studies noted increased risks for renal cell cancer, colorectal cancer, and other cancers.90,91 One study quotes up to a 31-fold increase in RCC risk for PTEN mutation carriers as compared to the general population.92
SMARCA4 truncating mutations cause rhabdoid tumor predisposition syndrome type 2. SMARCA4-associated tumors are highly aggressive and include atypical teratoid/rhabdoid tumors (AT/RT) of the central nervous system, malignant rhabdoid tumors of the kidney, and small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). The lifetime cancer risks for SMARCA4 mutation carriers has yet to be defined; however, age of onset and penetrance are extremely variable, with some carriers presenting prenatally while others remain unaffected through adulthood.93-96
STK11 germline mutations are associated with Peutz-Jeghers syndrome (PJS), an autosomal dominant disorder characterized by the development of gastrointestinal hamartomatous polyps, along with hyperpigmentation of the skin and mucous membranes. Overall, individuals affected with PJS have up to an 85% lifetime risk of developing cancer by the age of 70, with gastrointestinal and breast cancers being the most common.97,98 Individuals with PJS are also at elevated risk for tumors of the pancreas, lung, and, in females, ovarian tumors, specifically, sex cord tumors with annular tubules (SCTATs) and mucinous ovarian tumors.
TP53 is a tumor suppressor gene, and germline mutations within it are associated with Li-Fraumeni syndrome (LFS). An individual carrying a TP53 mutation has a 21-49% lifetime risk of developing cancer by age 30 and a lifetime cancer risk of 68-93%.99 The most common tumor types observed in LFS families include soft tissue and osteosarcomas, breast cancer, brain tumors (including astrocytomas, glioblastomas, medulloblastomas and choroid plexus carcinomas), and adrenocortical carcinoma (ACC); other cancers, including colorectal, gastric, ovarian, pancreatic, and renal, have also been reported.12,100 Studies have shown that a small percentage of women with early onset breast cancer that do not carry BRCA1 and BRCA2 mutations are identified to have mutations in TP53.56,101,102
Additional genes found on CancerNext-Expanded
The following genes are included in CancerNext-Expanded, but not in CancerNext:
AIP mutations cause familial isolated pituitary adenomas (FIPA), an autosomal dominant condition. These occur in a familial setting in the absence of multiple endocrine neoplasia 1 (MEN1), Carney complex, or other known inherited conditions. FIPA differs from MEN1 in terms of a lower proportion of prolactinomas and more frequent somatotropinomas in the FIPA cohort.103 Mutations in the AIP gene have been identified in 15-30% of cases of FIPA and have also been reported in individuals with sporadic pituitary adenomas.103,104 Compared to AIP mutation-negative individuals with pituitary adenomas, individuals with mutations are more likely to have aggressive disease and present earlier in life.103 The median age of diagnosis of AIP-related FIPA is 23 years and penetrance estimates range from 33-66%.103,105
ALK heterozygous germline mutations in the ALK gene are associated with familial predisposition to neuroblastic tumors including neuroblastoma, ganglioneuroblastoma, and ganglioneuroma.106 Germline mutations in ALK have also been implicated in medulloblastoma risk, but further study is necessary.107 Penetrance for neuroblastoma is variable, and is estimated to be up to 57% across studies.108
BAP1 mutations have been shown to cause a tumor predisposition syndrome characterized by uveal melanoma, cutaneous melanoma, renal cell carcinoma, asbestos exposure-induced mesothelioma, and nonmalignant melanocytic BAP1-mutated atypical intradermal tumors (MBAITs).109-112 Lifetime cancer risks are increased, but are not well defined.
BLM is a gene associated with Bloom syndrome, a rare autosomal recessive condition affecting multiple body systems. Studies have demonstrated an increased risk for breast cancer in women who carry a Slavic founder mutation (p.Q548*) in BLM, including a meta-analysis of BLM mutations that suggested a two- to five-fold increased risk for female breast cancer in carriers.113,114 Additionally, BLM mutations have also been associated with an increased risk for colorectal cancer; however, exact cancer risks are not currently available.115,116
CDKN1B Heterozygous germline alterations are associated with multiple endocrine neoplasia type 4 (MEN4), characterized by parathyroid, anterior pituitary, and neuroendocrine tumors.117 Nearly 100% individuals with CDKN1B mutations develop hyperparathyroidism, however, penetrance estimates for other features of this syndrome are not currently available.118 MEN4 and multiple endocrine neoplasia type 1 share similar phenotypes, and mutations in CDKN1B account for 1-3% of individuals with clinically diagnosed MEN1 lacking a germline mutation in the MEN1 gene.117,119
DICER1 mutations have been shown to cause a tumor predisposition syndrome associated with an increased risk for various benign and malignant tumors. Studies have demonstrated an increased risk for tumors including pleuropulmonary blastoma, cystic nephroma, ovarian sex cord stromal tumors (primarily Sertoli-Leydig cell tumors), multinodular goiter and thyroid cancer, embryonal rhabdomyosarcomas, ciliary body medulloepithelioma, nasal chondromesenchymal hamartomas, and pituitary blastoma, as well as various other tumor types. At this time, lifetime risks for each tumor type have not been well described.120-122
FANCC is a gene involved in the Fanconi anemia pathway, critical for DNA repair by homologous recombination. Carriers of FANCC mutations have been identified in high-risk breast cancer families.123 A study found an increased risk for breast cancer in female relatives of patients with Fanconi anemia type C (FA-C) who carried a FANCC mutation.124 Other studies have identified FANCC mutations in patients with apparently sporadic, early-onset pancreatic cancer.125-127 Lifetime cancer risk estimates are not currently available for mutation carriers.
FH is a gene associated with hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is characterized by an increased lifetime risk of developing papillary type 2 renal tumors, with a lifetime risk of up to 20% for renal cancer and nearly 98% risk of cutaneous and uterine leiomyomas/fibroids.129 HLRCC-associated renal tumors are more likely to present as unilateral solitary lesions, with about 20% of individuals identified in their forties at an age range of 17-75 years. Almost all female HLRCC mutation carriers have uterine fibroids, with a mean age of diagnosis at 30 years, and an age range of 18-52 years.16,22,128,129 Although uterine fibroids are common in the general population, the fibroids in women with HLRCC tend to be larger and more numerous. In addition, mutations in the FH gene have recently been reported in individuals with malignant pheochromocytomas (PCCs) and paragangliomas (PGLs).130,131
FLCN gene mutations cause Birt-Hogg-Dubé (BHD), an autosomal dominant hereditary renal cancer syndrome. A classic triad of findings characterizes BHD, which includes cutaneous fibrofolliculomas (benign skin tumors), pulmonary cysts, and renal tumors.16,132 Pulmonary cysts are found in approximately 80% of affected individuals, while bilateral renal tumors affect up to 34% of individuals. Secondary clinical findings can include spontaneous pneumothoraces, colorectal adenomas, parathyroid adenomas, neural tissue tumors, lipomas, angiolipomas, and connective tissue abnormalities. Individuals with BHD have about a 34% lifetime risk for renal cancer, most frequently diagnosed in the fifties.132-134 Additionally, male FLCN mutation carriers are twice as likely to be affected as female carriers.135,136 Approximately 50% of BHD-related renal tumors manifest as a chromophobe/oncocytic hybrid: 34% chromophobe, 9% clear cell, 5% oncocytoma, and 2% papillary.137
GALNT12 mutations have been identified in individuals with colorectal cancer and polyps. Carriers of GALNT12 mutations may be at an increased lifetime risk for colorectal cancer; however, lifetime cancer risk estimates are not currently available.138,139
HOXB13 encodes a transcription factor involved in epidermal differentiation and prostate gland development. Multiple studies have associated a recurrent HOXB13 mutation, p.G84E, with an increased risk for early-onset prostate cancer, however, lifetime cancer risk estimates are not currently available for mutation carriers.140-142 Data are insufficient to support increased cancer risks for other HOXB13 alterations at this time.
MAX is a tumor suppressor gene associated with PCC susceptibility. In one study of twelve MAX mutation carriers with PCC, 25% of patients showed metastasis, suggesting that, similar to SDHB, MAX mutations are associated with an increased metastatic potential.143 The exact PCC lifetime risk is not yet established for MAX mutation carriers. Seemingly sporadic PCCs may be due to paternal transmission of the mutant allele.24,26,143
MEN1 mutations cause multiple endocrine neoplasia type 1 (MEN1) and familial isolated hyperparathyroidism (FIHP). FIHP is defined by primary hyperparathyroidism as the sole endocrinopathy in a family.144 In contrast, MEN1 is characterized by primary hyperparathyroidism due to parathyroid adenomas (present in over 90% of affected individuals), gastro-entero-pancreatic neuroendocrine tumors (in 30-70%), pituitary adenomas (in 30-60%), adrenocortical tumors (15-50%), bronchial and thymic carcinoids (up to 10%), facial angiofibromas, collagenomas, and lipomas.145-150 The majority of patients (94%) carrying a mutation in the MEN1 gene exhibit clinical or biochemical symptoms by age 50.151
MET is a proto-oncogene associated with hereditary papillary renal carcinoma (HPRC). HPRC is an autosomal dominant disorder with high penetrance, characterized by increased risk for bilateral (or multifocal type 1) papillary renal cancer. HPRC-associated renal cancer has a median age of onset of 60-80 years.16,17,129 Furthermore, HPRC renal tumors show frequent somatic trisomy of chromosome 7, and earlier-onset carcinoma can be attributed to germline missense mutations in the tyrosine kinase domain of the MET proto-oncogene.152
MITF is a gene implicated in melanoma and renal cell carcinoma (RCC) development pathways.153,154 As such, MITF mutation carriers have an increased predisposition to developing melanoma and/or RCC. A specific mutation with unique functional consequences, p.E318K, has been detected at increased frequency in both melanoma and RCC cohorts.153,154 MITF mutation carriers are estimated to have a 2-8 fold increased risk for melanoma and a 5-fold increased risk for RCC as compared to the general population.153,155
NF2 heterozygous germline pathogenic mutations cause neurofibromatosis type 2 (NF2), characterized by development of multiple nerve sheath tumors, most notably bilateral vestibular schwannomas (present in over 90% of individuals), as well schwannomas of other cranial nerves (in 24-51%), intracranial meningiomas (in 45-58%), and spinal tumors including meningiomas, schwannomas, gliomas, ependymomas, and rarely astrocytomas (combined 63-90%).156 Approximately 50% of all NF2 mutations are inherited while the remaining 50% are de novo events. Of the NF2 mutations that are de novo events, up to 30% are mosaic.157
PHOX2B functions as a transcription factor involved in the development of several major noradrenergic neuron populations and the determination of neurotransmitter phenotype. Expansion of a 20 amino acid polyalanine tract in this protein by 5-13 aa has been associated with congenital central hypoventilation syndrome (CCHS), characterized by apparent hypoventilation due to autonomic nervous system dysregulation (ANSD) as well as abnormalities of neural crest-derived structures, such as Hirschsprung disease (HSCR), and tumors of neural crest origin.158 Heterozygous germline mutations outside the polyalanine repeat region predispose to neuroblastic tumors such as neuroblastoma, ganglioneuroblastoma, and ganglioneuroma, with or without other neurocristopathies of CCHS and HSCR.159 Genotype-phenotype correlations are under study to help better define disease mechanisms and the extent of overlap of the various phenotypes associated with PHOX2B mutations.160
POT1 heterozygous germline alterations have been identified in familial and unselected cases of glial tumors such as glioma, astrocytoma, and oligodendroglioma, and appear to demonstrate incomplete penetrance.161,162 Lifetime cancer risk estimates for POT1 mutation carriers are not currently available.
PRKAR1A heterozygous germline pathogenic mutations cause Carney complex, which is characterized by primary pigmented nodular adrenocortical disease (PPNAD, present in 26-60% of individuals), pituitary adenoma (in 10-12%), cardiac myxoma (in 32-53%), skin and breast myxomas (in 20-33%), thyroid nodules (in 25%) and/or carcinoma (in 2-5%), large-cell calicifying Sertoli cell tumor (in 33-41%), and psammomatous melanotic schwannomas (in 8-10%).163-166
PTCH1 mutations cause nevoid basal cell carcinoma syndrome (NBCCS), also referred to as Gorlin syndrome. NBCCS/Gorlin syndrome is an autosomal dominant condition with a de novo mutation rate of 20-30%, and up to 90% of affected individuals develop basal cell carcinoma. In addition, NBCCS can cause odontogenic keratocysts, congenital skeletal anomalies, cerebral calcifications, macrocephaly, polydactyly, intellectual disability, palmar epidermal pits, and cardiac and ovarian fibromas.167-171 Up to 5% of children with NBCCS develop medulloblastoma, also called primitive neuroectodermal tumor (PNET), most often the desmoplastic subtype. The diagnosis of NBCCS has historically been made based on clinical features.
RET is a proto-oncogene associated with multiple endocrine neoplasia type 2 (MEN2). MEN2 is an autosomal dominant disorder characterized by the presence of benign or malignant endocrine system tumors. MEN2 is divided into three clinical subtypes: MEN2A (>90% of patients), MEN2B, and familial medullary thyroid carcinoma (FMTC). MEN2-associated PCCs are often multifocal and bilateral, with a median age of diagnosis between 30-40 years.24,26,172
RB1 encodes a 928 amino acid nuclear phosphoprotein pRB, which functions as a negative regulator of the cell cycle and cell proliferation. Heterozygous pathogenic mutations in RB1 cause retinoblastoma, a malignant tumor of the developing retina. Individuals with germline mutations in RB1 typically present with bilateral tumors, though some individuals develop unilateral or trilateral (involving the pineal gland) disease. The majority of mutations is highly penetrant and confers a 90% risk for retinoblastoma.173 However, a subset of mutations is moderately penetrant and result in lower and variable risk of disease.174 Individuals with hereditary retinoblastoma are at increased risk to develop second primary malignancies including osteosarcomas, soft tissue sarcomas, and melanoma, as well as other common epithelial malignancies. Risks for such malignancies vary based on laterality of tumor, family history, age at initial diagnosis, and treatment course.175,176
SDHA, SDHB, SDHC, SDHD, and SDHAF2 are all genes associated with hereditary paraganglioma and pheochromocytoma (PGL/PCC) syndrome. Germline mutations in these genes have been associated with susceptibility to head and neck paragangliomas (HNPGLs), extra-adrenal PGLs/PCCs and, rarely, renal cell carcinoma (RCC) with gastrointestinal stromal tumors (Carney-Stratakis syndrome).177 SDHB associated RCC can be of varied histology with reported cases of clear cell, papillary, granular, and mixed.178,179 The exact lifetime risk for PCC is not yet established for SDHB mutation carriers.180 The SDHD and SDHAF2 genes are subject to the effects of imprinting (parent-of-origin effects), and cancer risk is correlated with paternal transmission.181-183 Mutations in the SDH genes have also been associated with PTEN mutation-negative Cowden syndrome.184
SMARCB1 heterozygous germline pathogenic mutations cause rhabdoid tumor predisposition syndrome type 1 (RTPS1) and schwannomatosis. Individuals with RTPS1 are at risk to develop atypical teratoid/rhabdoid tumors of the CNS and malignant rhabdoid tumors of the kidney.185 Age of onset and penetrance are extremely variable, with some carriers presenting at birth while others remain unaffected through adulthood.186 Approximately 5% of individuals with schwannomatosis due to SMARCB1 mutation also develop meningiomas.185 SMARCB1 mutations are thought to account for 35% of AT/RT, 48% of familial schwannomatosis, and 10% of sporadic schwannomatosis.185,186 It is believed that individuals with non-truncating mutations in SMARCB1 have a low risk for AT/RT, but genotype-phenotype correlations are still under study to help better define disease mechanisms and the extent of phenotypic overlap of the three syndromes associated with SMARCB1 mutations.185
SMARCE1 heterozygous loss-of-function alterations such as truncations, frameshifts, and gross deletions cause predisposition for multiple spinal and cranial clear cell meningiomas.187,188 The lifetime risk for clear cell meningiomas in SMARCE1 mutation carriers has yet to be defined; however, age of onset and penetrance are extremely variable, with some carriers presenting in early childhood while others remain unaffected through adulthood.188
SUFU heterozygous germline pathogenic mutations cause nevoid basal cell carcinoma syndrome (NBCCS), also referred to as Gorlin syndrome. NBCCS/Gorlin syndrome is a genetically and clinically heterogeneous condition characterized by multiple basal cell carcinomas, jaw keratocysts, skeletal anomalies, palmar and plantar pits, calicification of the falx cerebri, coarse facial features, macrocephaly, increased risk for childhood-onset desmoplastic medulloblastoma, ovarian and cardiac fibromas, ocular anomalies, and cleft lip and palate.189 Approximately 5% of individuals with NBCCS will develop medulloblastoma, however current data suggests the risk is higher (~30%) in individuals with mutations in SUFU than in other genes that cause NBCCS.190,191 Some individuals with mutations in SUFU develop isolated medulloblastoma without other symptoms of NBCCS.191 SUFU has also been implicated in familial meningioma.192
TMEM127 is a proposed tumor suppressor gene associated with PGL/PCC susceptibility.193 TMEM127 mutations demonstrate an autosomal dominant pattern of inheritance with unknown penetrance.24,26 TMEM127-associated PCCs can present bilaterally or unilaterally, and may also be found in patients with no family history of PCC.180,193 One study reported TMEM127 mutations in 2 of 48 patients with PGL.193
TSC1 and TSC2 are genes associated with tuberous sclerosis complex (TSC), a multi-system neurocutaneous disorder characterized by presence of benign hamartomas in multiple tissues and organs, seizures, and intellectual disability.194 Benign hamartomas can be found in the heart (rhabdomyomas), brain (astrocytomas), kidneys (angiomyolipomas), skin, eyes, lungs (pulmonary lymphangioleimyomatosis), skeleton, and endocrine glands.194-198 The lifetime risk of renal cancer development in TSC is 2-5%.195
VHL mutations are associated with von Hippel-Lindau disease (VHL). VHL is an autosomal dominant cancer predisposition syndrome with about a 20% de novo mutation rate and an estimated incidence of 1 in 36,000.129 VHL is characterized by renal tumors, adrenal pheochromocytoma (PCC), retinal angiomas, central nervous system hemangioblastomas, pancreatic cysts, and neuroendocrine tumors. The associated lifetime risk of RCC in those with VHL is estimated at 25-70%, depending on disease subtype. VHL-associated renal tumors tend to be earlier-onset (average age of diagnoses is 39 years) and multifocal.199 Published literature supports that patients carrying a partial germline VHL gene deletion have a higher RCC risk than those carrying full-gene deletions.17,129
XRCC2 is a gene involved in the Fanconi anemia pathway, critical for DNA repair by homologous recombination. Female and male individuals with breast cancer have been found to carry monoallelic mutations in XRCC2.200-202 Currently, breast cancer lifetime risk estimates are not available for mutation carriers.
Indications for Testing
CancerNext-Expanded may be appropriate in the following situations, combined with common red flags for hereditary cancer:
Common Red Flags for Hereditary Cancer
*On the same side of the family
If increased risk of a hereditary cancer syndrome is suspected, the American Congress (formerly College) of Obstetricians and Gynecologists (ACOG) recommends referral to a specialist in cancer genetics or a healthcare provider with expertise in genetics for complete hereditary cancer risk assessment, which may lead to genetic testing.140 Establishing a molecular diagnosis can help guide preventive measures, direct surgical options and estimate personal and familial cancer risk.
Benefits of Testing
Identifying patients with an inherited susceptibility for certain cancers can help with medical management. For example, this information can:
CancerNext-Expanded analyzes 67 genes (listed above). 65 genes (excluding EPCAM and GREM1) are evaluated by next generation sequencing (NGS) or Sanger sequencing of all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. In addition, sequencing of the promoter region is performed for the following genes: PTEN (c.-1300 to c.-745), MLH1 (c.-337 to c.-194), and MSH2 (c.-318 to c.-65). For POLD1 and POLE, missense variants located outside of the exonuclease domains (codons 311-541 and 269-485, respectively) are not routinely reported. For MITF, only the status of the c.952G>A (p.E318K) alteration is analyzed and reported. The inversion of coding exons 1-7 of the MSH2 gene and the BRCA2 Portuguese founder mutation, c.156_157insAlu (also known as 384insAlu) are detected by NGS and confirmed by PCR and agarose gel electrophoresis. For ALK, only variants located within the kinase domain (c.3286-c.4149) are reported. For PHOX2B, the polyalanine repeat region is excluded from analysis. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Additional Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.203 Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of 66 genes (excluding MITF) using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray. For GREM1, only the status of the 40kb 5’ UTR gross duplication is analyzed and reported. For APC, all promoter 1B gross deletions as well as single nucleotide substitutions within the promoter 1B YY1 binding motif are analyzed and reported. If a deletion is detected in exons 13, 14, or 15 of PMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene, PMS2CL, will be performed to determine if the deletion is located in the PMS2 gene or pseudogene.
CancerNext-Expanded can detect >99.9% of described mutations in the included genes listed above, when present (analytic sensitivity).
|TEST CODE||TEST NAME||TURNAROUND TIME (days)|
|8874||CancerNext-Expanded||14 - 21|