BRAF-Related Disorders via the BRAF Gene

Cardio-facio-cutaneous syndrome (CFCS, OMIM 115150) is a rare developmental disorder characterized by distinctive facial appearance, congenital cardiac and ectodermal abnormalities, postnatal growth failure, feeding difficulties with failure to thrive, and neurological findings. Facial features include high forehead; short, upturned nose with a low nasal bridge; prominent external ears that are posteriorly angulated; and ocular hypertelorism. The most common cardiac abnormalities include pulmonic stenosis and atrial septal defects. Ectodermal abnormalities are heterogeneous in features and severity. They include café au lait spots, erythema, keratosis, ichthyosis, eczema, sparse and brittle hair, and nail dystrophy. The neurological findings include seizures, hypotonia, macrocephaly and various degrees of mental and cognitive delay (Reynolds et al. Am J Med Genet 25:413-427, 1986).

Noonan syndrome (NS, OMIM 163950) is a relatively common developmental disorder. NS is characterized by dysmorphic facial features, growth and congenital heart defects, and musculoskeletal abnormalities. Cardiac abnormalities are found in up to 80% of patients and include pulmonary valve stenosis, atrial septal defect, atrioventricular canal defect, and hypertrophic cardiomyopathy. Musculoskeletal abnormalities include short stature, chest deformity with sunken or raised sternum, and short webbed neck. Several additional abnormalities have been described and include renal, genital, hematological, neurologic, cognitive, behavioral, gastrointestinal, dental, and lymphatic findings. Intelligence is usually normal; however, learning disabilities may be present. NS is characterized by an extensive clinical heterogeneity, even among members of the same family. Diagnosis is often made in infancy or early childhood. Symptoms often change and lessen with advancing age. Infants with NS are at risk of developing juvenile myelomonocytic leukemia (JMML OMIM 607785). The prevalence of NS is estimated at 1 in 1000-2500 births worldwide (Allanson et al. Am J Med Genet 21:507-514, 1985; Romano et al. Pediatrics 126:746-759, 2010).

LEOPARD syndrome (multiple lentigines, electrocardiographic-conduction abnormalities, ocular hypertelorism, pulmonary stenosis, abnormal genitalia, retardation of growth, sensorineural deafness, OMIM 151100) is a rare congenital developmental disorder characterized by skin pigmentation anomalies including multiple lentigines and café au lait spots, hypertrophic cardiomyopathy, pulmonary valve stenosis, and deafness. Other less common features include short stature, mild mental retardation, and abnormal genitalia (Legius et al. J Med Genet 39:571-574, 2002; Sarkozy et al. J Med Genet 41:e68, 2004).

CFCS is caused by variants in four genes within the RAS/MAPK pathway: BRAF, MAP2K1, MAP2K2, and KRAS (Rodriguez-Viciana et al. Science 311:1287-1290, 2006; Niihori et al. Nat Genet 38:294-296, 2006). Over 37 BRAF variants were detected in patients with CFCS. They are the most common cause of CFCS, and account for ~75% of all cases genotyped. Most causative variants are missense. A few small deletions have also been reported. All variants reported to date have been de novo. The penetrance is complete in patients with CFCS (Rauen, GeneReviews, 2010).

NS is caused by gain of function variants in various genes within the RAS/MAPK pathway, including BRAF. These variants appear to activate the gene product (SHP2 protein). To date, seven RAS/MAPK genes (PTPN11, SOS1, RAF1, KRAS, SHOC2, BRAF, and NRAS) have been involved in patients with NS. BRAF variants were reported in ~2% of all NS cases genotyped (Allanson and Roberts, GeneReviews, 2011). Only four different missense variants were reported (Sarkozy et al. Hum Mutat 30:695-702, 2009). Although de novo variants are found in a substantial fraction of patients, familial cases have been reported. In these families, NS is inherited in an autosomal dominant manner with variable expressivity (Romano, Pediatrics 126:746-759, 2010).

LEOPARD syndrome is caused by defects in three genes within the RAS/MAPK: PTPN11, RAF1, and BRAF (Digilio et al. Am J Hum Genet 71:389-394, 2002; Pandit et al. Nat Genet 39:1007-1012, 2007; Sarkozy, Hum Mutat 30: 95-702, 2009). Unlike NS, LEOPARD syndrome variants act through a dominant negative effect, which appears to disrupt the function of the wild-type gene product (SHP2 protein; Jopling et al. PLOS Genetics 3:e225, 2007). Only two different BRAF missense variants were reported in patients with LEOPARD syndrome (Sarkozy, 2009; Koudova et al. Eur J Med Genet 52:337-340, 2009). Parents of LEOPARD patients are often asymptomatic, and de novo variants are common. However, familial cases have been reported. In these families, affected relatives are diagnosed only after the birth of a visibly affected child, and the disease is transmitted in an autosomal dominant manner with variable penetrance and expressivity (Gelb and Tartaglia, GeneReviews, 2010). Genotype-phenotype correlations have been proposed (see for example Limongelli et al. Am J Med Genet A 146:620-628,2008). Somatic BRAF variants have been implicated in several human cancers.

This test will detect causative variants in ~75% of CFCS patients, ~5% of LS patients, and ~2% of NS patients.

This test provides full coverage of all coding exons of the BRAF gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.