Somatic Overgrowth & Vascular Malformation

GENETIC DIAGNOSTIC LABORATORY UPENN SCHOOL OF MEDICINE DEPARTMENT OF GENETICS 415 ANATOMY & CHEMISTRY BLDG 3620 HAMILTON WALK PHILADELPHIA, PA 19104 (p) 215.573.9161 (f) 215.573.5940

Genetic Diagnostic Laboratory Department of Genetics Department of Genetics SOMATIC OVERGROWTH & VASCULAR MALFORMATION GENETIC TESTING

General: This test provides analysis of 34 genes associated with somatic overgrowth and vascular malformation features such as segmental overgrowth, megalencephaly, various vascular malformations, epidermal nevi, macrodactyly, and/or polydactyly. See Table 2 for genes and associated conditions. Most mutations in the genes analyzed are somatic in origin. These mutations are often post-zygotic leading to mosaicism and are poorly detected in the blood. These mutations are better detected in a clearly affected tissue (skin, muscle, adipose, central nervous system). Submission of affected tissue is strongly recommended to increase sensitivity. The cost of testing includes up to two samples (additional samples may be tested for an additional cost- please call the lab for this information).

Somatic Overgrowth NGS Panel Assay and Limitations: Capture-based target enrichment and Next Generation Sequencing on Illumina MiSeq platform including 34 genes: AKT1, AKT2, AKT3, BRAF, CCM2, CCND2, CDKN1C, FGFR1, FGFR2, FGFR3, FLT4, GLMN, GNA11, GNA14, GNAQ, HRAS, IDH1, IDH2, KDR, KRAS, KRIT1, MAP2K1, MAP3K3, MTOR, NRAS, PDCD10, PIK3CA, PIK3R1, PIK3R2, PTEN, RASA1, SMO, STAMBP, TEK. See Table 2 for genes and associated conditions.

The limit of variant allele detection is 1% at 2500x read depth and the threshold for mutation detection is set at 10 reads without strand bias. Molecular barcode technology is used to distinguish low level true variants from amplification and sequencing errors. This technology cannot reliably detect mutations at a read depth coverage below 100x. Confirmation of mutations found via NGS may be performed by droplet digital PCR or Sanger Sequencing.

Clinical Utility: Confirmation of a clinical diagnosis, assist in determination of appropriate medical management, identification of at risk family members, and/or prognostic evaluation.

Table 1: Testing Options Name of Test Turnaround Time Cost CPT Codes Somatic Overgrowth NGS Panel 4 weeks $3000 81479 UP TO 2 SAMPLES PRENATAL Somatic Overgrowth NGS Panel 2-4 weeks $3100 81479, 81265

415 Anatomy-Chemistry Building, 3620 Hamilton Walk, Philadelphia, PA 19104 Tel: 215-573-9161 / Fax: 215-573-5940 / Web: www.med.upenn.edu/genetics L:\GDL Forms\Forms in Development\OVGv3\SOFT LAUNCH Versions\Somatic OVGv3 Info Form 02.24.2020.docx GENETIC DIAGNOSTIC LABORATORY UPENN SCHOOL OF MEDICINE DEPARTMENT OF GENETICS 415 ANATOMY & CHEMISTRY BLDG 3620 HAMILTON WALK PHILADELPHIA, PA 19104 (p) 215.573.9161 (f) 215.573.5940

Genetic Diagnostic Laboratory Department of Genetics Department of Genetics Table 2: Gene and Disease Information Gene/ OMIM Related associated condition(s) Location AKT1 164730 Proteus syndrome [#176920]: Progressive asymmetric overgrowth of 14q32.33 body parts, cerebriform connective tissue nevi, epidermal nevi, lipomas, and vascular malformations. Cowden syndrome type 6 [#615109]: Multiple noncancerous, tumor- like growths called hamartomas and an increased risk of developing certain cancers. AKT2 164731 Hypoinsulinemic hypoglycemia with hemihypertrophy [#240900] 19q13.2 Diabetes mellitus type II [#125853] AKT3 611223 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus 1q43-44 syndrome [#615937]: Abnormal growth and development of the brain, leading to megalencephaly, brain malformations and overgrowth. Hemimegalencephaly BRAF 164757 Somatic Nevi4,5,10,11 7q34 Cardiofaciocutaneous syndrome [#115150]: Affects heart, face, and skin/hair. Skin abnormalities may include keratosis pilaris. Face is typically broad and long. Noonan syndrome [#613706]: Affects face, stature, and heart. CCM2 607929 Cerebral cavernous malformations-2 [#603284]: collections of small 7p13 blood vessels (capillaries) in the brain that are enlarged and irregular in structure. CCND2 123833 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus 12p13.32 syndrome [#615938]: Abnormal development of the brain, leading to megalencephaly and other abnormalities of the brain structure. CDKN1C 600856 Beckwith-Wiedemann Syndrome [#130650]: Pediatric overgrowth 11p15.4 condition with increased risk of tumor development, specifically Wilms tumors. Macroglossia, hemihypertrophy, omphalocele. IMAGE Syndrome [#614732]: IUGR, metaphyseal dysplasia, congenital adrenal hypoplasia, genital anomalies. FGFR1 136350 Encephalocraniocutaneous lipomatosis [#613001]: A neurocutaneous 8p11.23 disorder with patchy and asymmetric eye, skin, and CNS anomalies. The most common skin finding is nevus psiloliparus of the scalp. FGFR2 176943 Schimmelpenning Syndrome: [#163200] linear nevus sebaceous. 10q26.13 Multiple craniosynostosis and dysplasia syndromes: Antley Bixler Syndrome [#207410], Alpert Syndrome [#101200], Beare-Stevenson Syndrome [#123790], Pfeiffer Syndrome [#101600], Crouzon Syndrome [#123500], Saethre-Chotzen Syndrome [#101400]. Vascular disease7,8,9

Genetic Diagnostic Laboratory Department of Genetics Department of Genetics Table 2 Continued: FGFR3 134934 Somatic epidermal nevus [#162900]: Epidermal nevi caused by somatic 4p16.3 mutations that typically follow Blaschko lines. Multiple craniosynostosis and dysplasia syndromes: Achondroplasia [#100800], ], Crouzon Syndrome with acanthosis nigricans [#612247], Hypochondroplasia [#146000], Thanatophoric dysplasia [#187600/01], Muenke Syndrome [#602849] FLT4 136352 Somatic hemangiomas [#602089]: Benign, highly proliferative lesions 5q35.3 with aberrant localized growth of capillary endothelium. Lymphatic malformations [#153100]: Chronic edema with possible nail/skin changes. GLMN 601749 Glomuvenous malformations [#138000]: Venous malformations with 1p22.1 glomus (rounded) cells or glomangiomas. Cobble stone in appearance, and painful on palpitation. GNA11 139313 Sturge Weber syndrome [#185300]: Facial port-wine stains, 19p13.3 leptomeningeal angiomatosis, capillary malformations of the choroid, seizures, and glaucoma. Diffuse cutaneous capillary malformation with mild overgrowth3 GNA14 604397 Kaposiform hemangioendothelioma3 9q21.2 Chorea-acanthocytosis [#200150]: Neurodegeneration and morphologically abnormal red cells. GNAQ 600998 Sturge Weber syndrome [#185300]: Facial port-wine stains, 9q21.2 leptomeningeal angiomatosis, capillary malformations of the choroid, seizures, and glaucoma. Somatic capillary malformations [#163000]: Somatic capillary malformations that may be present at birth and tend to grow with the individual, do not regress spontaneously, and show normal rates of endothelial cell turnover Diffuse cutaneous capillary malformation with mild overgrowth3 HRAS 190020 Schimmelpenning-Feuerstein-Mims syndrome [#163200]: linear 11p15.5 sebaceous nevus syndrome: sebaceous nevi (seen on face and along Blaschko lines) and ipsilateral abnormalities of the CNS. May have skeletal anomalies. Costello syndrome [#218040]: Characteristic face, short stature, and hand posture with feeding difficulty and FTT. Somatic epidermal nevus [#162900]: Epidermal nevi caused by somatic mutations that typically follow Blaschko lines. IDH1 147700 Maffucci Syndrome12,13 [#614569]: Multiple enchondromas and soft 2q34 tissue hemangiomas, usually presenting in childhood. May also have lymphangiomas. Somatic susceptibility to gliomas [#137800] IDH2 147650 Maffucci Syndrome12,13 [#614569]: Multiple enchondromas and soft 15q26.1 tissue hemangiomas, usually presenting in childhood. May also have lymphangiomas. Somatic susceptibility to gliomas [#137800]

Genetic Diagnostic Laboratory Department of Genetics Department of Genetics Table 2 Continued: KDR 191306 Somatic hemangiomas [#602089]: Benign, highly proliferative lesions 4q12 with aberrant localized growth of capillary endothelium. KRAS 190070 Arteriovenous malformations of the brain due to somatic mutations 12p12.1 [#108010]. Pyogenic granuloma3 Cardiofaciocutaneous syndrome [#615278]: Developmental disorder affecting many parts of the body, mainly heart, face, and skin/hair. Skin abnormalities may include keratosis pilaris. Face is typically broad and long. Noonan syndrome [#609942]: Affects many parts of the body including face, stature, and heart. KRIT1 604214 Cerebral cavernous malformations-1 [#116860]: Vascular 7q21.2 malformations of the CNS, may cause seizure, hemorrhage, or neurologic deficit. MAP2K1 176872 Arteriovenous malformation3 15q22.31 Cardiofaciocutaneous syndrome [#615279]: Developmental disorder involving heart, face, and skin/hair. MAP3K3 602539 Verrucous venous malformation3 17q23.3 MTOR 601231 Facial Cortical Dysplasia [#607341]: Cerebral development 1p36.22 malformation resulting in epilepsy. Smith-Kingsmore Syndrome [#616638]: Intellectual disability with macrocephaly, seizures, umbilical hernia, frontal bossing, midface hypoplasia, and hypertelorism. Unexplained overgrowth2 NRAS 164790 Somatic epidermal nevus4 [#162900]: Epidermal nevi caused by 1p13.2 somatic mutations that typically follow Blaschko lines. Congenital Melanocytic Nevi5 [#137550]: Pigmentary skin defects, including 1 or more large legion with many smaller “satellite” pigment lesions, that are apparent at birth. Neurocutaneous Melanosis [#249400]: Melanin producing cells present in the brain parenchyma or leptomeninges and can cause neurological abnormalities. Noonan syndrome [#613224]: Affects face, stature, and heart. Schimmelpenning-Feuerstein-Mims syndrome [#163200]: linear sebaceous nevus syndrome: sebaceous nevi (often seen on face and along Blaschko lines) and ipsilateral abnormalities of the CNS. May have skeletal anomalies. Pyogenic granuloma3 PDCD10 609118 Cerebral cavernous malformations-3 [#603285]: Vascular 3q26.1 malformations of the CNS.

Genetic Diagnostic Laboratory Department of Genetics Department of Genetics Table 2 Continued: PIK3CA 171834 CLOVES syndrome3 [#612918]: Congenital lipomatous overgrowth, 3q26.32 vascular malformations, epidermal nevi and spinal/skeletal anomalies Megalencephaly-capillary malformation-polymicrogyria syndrome3 [MCAP; #602501]: Abnormal development of the brain, leading to megalencephaly and other abnormalities of the brain structure Somatic epidermal nevus [162900]: Epidermal nevi caused by somatic mutations that typically follow Blaschko lines. PIK3R1 171833 SHORT syndrome [#269880]: Stature, hyperextensibility of joints or 5q13.1 inguinal hernia, ocular depression, Reiger anomaly, teething delay, partial lipodystrophy, insulin resistance, and delays. Somatic mutations have been seen in glioblastomas. PIK3R2 603157 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus 19p13.11 Syndrome [MPPH; #603387]: Abnormal development of the brain, leading to megalencephaly and other abnormalities of the brain structure. Unexplained overgrowth2 PTEN 601728 Cowden syndrome type 13 [#158350]: A hamartomatous disorder 10q23.31 characterized by macrocephaly, facial trichilemmomas, papillomatous papules, and an increased risk for the development of breast, thyroid, and endometrial carcinoma. Macrocephaly Autism Syndrome [#605309]: Macrocephaly with delayed psychomotor development resulting in autistic behavior or intellectual disability. Unexplained overgrowth2 RASA1 139150 Capillary Malformation-Arteriovenous Malformation 13 (#608354): 5q14.3 Atypical capillary malformations including arteriovenous malformations and fistulas. Susceptibility to Basal Cell Carcinoma [#605462] SMO 601500 Curry-Jones Syndrome [#601707]: A multisystem disorder with patchy 7q32.1 skin lesions, polysyndactyly, cerebral malformations, craniosynostosis, colobomas, micropthalmia, and intestinal malrotation. Susceptibility to Basal Cell Carcinoma [#605462] STAMBP 606247 Microcephaly-Capillary Malformation Syndrome [#614261]: Severe 2p13.1 progressive microcephaly, epilepsy, developmental delay, and multiple small capillary malformations. TEK 600221 Multiple Cutaneous and Mucosal Venous malformations [#600195]: 9p21.2 Small, multifocal cutaneoumucosal venous malformation lesions.

Genetic Diagnostic Laboratory Department of Genetics Department of Genetics References: 1 Cohen MM Jr. 2013. The AKT genes and their roles in various disorders. Am J Med Genet Part A 161A:2931–2937. 2 Keppler-Noreuil KM, Parker VE, Darling TN, Martinez-Agosto JA. 2016. Somatic overgrowth disorders of the PI3K/AKT/mTOR pathway & therapeutic strategies. Am J Med Genet Part C Semin Med Genet 172C:402–421. 3 Siegel DH, et. Al. Analyzing the Genetic Spectrum of Vascular Anomalies with Overgrowth via Cancer Genomics. J of Investigative Dermatology. 2018. 138:957-967. DOI:10.1016/j.jid.2017.10.033 4 Yazdi, etal. Mutations of the BRAF gene in benign and malignant melanocytic lesions. Soc of inves derm. 2003. 5 Linares, et al. Congenital melanocytic nevus syndrome: A case series. Actas dermosifiliogr. 2017;108:e57-62. 6 Mirzaa G, Parry DA, Fry AE, et al. De novo CCND2 mutations leading to stabilization of cyclin D2 cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome. Nat Genet. 2014;46(5):510–515. doi:10.1038/ng.2948 7 10.1152/ajpcell.00193.2002 FGFR2 promotes microvessel formation from mouse embryonic aorta. 8 10.1172/JCI11724. Cellular markers that distinguish the phases of hemangioma during infancy and childhood. 9 Unpublished data from UPenn &/or CHOP. 10 Celebi, et al. 2004. Evaluation of germline cdkn2a, arf, cdk4, pten, and braf alterations in atypical mole syndrome. 11 Polluck 2002 high frequencing of braf muts in nevi. 12 Amary, 2011. Nat gen. Ollier dx and maffucci sx are caused by somatic mosaic muts in IDH1 and IDH2 13 Pansuriya et al.2011.nat gen.somatic mosaic idh1 and idh2 muts are assd w enchondroma and spindle cell hemangioma in Ollier dx and maffucci sx.