Molecular Cytogenetic Biochemical

TesT Menu Diagnostic Laboratories

Lab Directors & Genetic Counselors...................2Molecular Diagnostic Lab Next Generation Sequencing Panels.............3Biochemical Diagnostic Lab Enzyme Panels..................................................7 Individual Enzymes..........................................8 Analytes............................................................8 Monitoring Tests............................................8Cytogenetic Laboratory Microarrays....................................................9 Chromosome Analysis....................................9 FISH for Congenital Abberations..................9 Oncology Mutation Analysis.........................9 Hematological Studies.................................10 FISH Hemotology Panels..............................10 Individual Probes..........................................10

Table of ConTenTs

MoleCular

Jennifer A. Lee, PhD, FACMG Lead Molecular Director

Fatima Abidi, PhD Technical Director

Julie R Jones, PhD, FACMG Director of Clinical Genomics

Sequencing Program

bioCheMiCal

Tim Wood, PhD, FACMG Director

Laura Pollard, PhD, FACMG Associate Director

Taraka Donti, PhDAssistant Director

CyTogeneTiC

Barbara DuPont, PhD, FACMG Senior Director

Alka Chaubey, PhD, FACMG Director

Mike Friez, PhD, FACMG Director of Diagnostic Labs

lab DireCTors

geneTiC Counselors

Robin Fletcher, MS, CGCLaboratory Genetic Counselor

Kellie Walden, MS, CGCLaboratory Genetic Counselor

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Next Generation Sequencing

Aortic Dysfunction or Dilation and Related Disorders Panel 20 genes- Arterial Hypertension Panel 11 genes- Bardet-Biedl Syndrome Panel 26 genes- Brugada Syndrome Panel 18 genes

Comprehensive Cardiac Panel 108 genes+ Comprehensive Pulmonary Panel 93 genes- Cone-Rod Dystrophy Panel 37 genes- Congenital Stationary Night Blindness Panel 14 genes

Connective Tissue Disroders Panel 35 genesCornelia de Lange Panel 5 genesCraniosynostosis Panel 8 genesDilated Cardiomyopathy (DCM)/Arrhythmogenic Cardiomyopathy Panel 51 genesEpilepsy/Seizure Panel 145 genesHearing Loss Panel 91 genes

- Hermansky-Pudlak Syndrome and Pulmonary Fibrosis Panel 25 genesHypertrophic Cardiomyopathy Panel 20 genes

- Leber Congenital Amaurosis Panel 24 genes- Long QT Panel 16 genes

Lysosomal Storage Disease Panel 75 genes- Macular Degeneration 24 genes

Neuronal Ceroid Lipofuscinoses Panel 9 genesNon-immune Hydrops Panel 87 genes

- Ocular Albinism and Hermansky Pudlak Panel 17 genes- Optic Atrophy and Early Glaucoma Panel 34 genes

Overgrowth/Macrocephaly Panel 16 genes- Peroxisome Biogenesis Disorders Panel 12 genes+ Primary Ciliary Dyskinesia and Cystic Fibrosis Panel 42 genes

RASopathy Panel 23 genes- Retinitis Pigmentosa Panel 91 genes

Rett/Angelman Syndrome 2nd Tier Sequencing Panel 21 genesRhabdomyolysis and Metabolic Myopathies Panel 47 genesSkeletal Dysplasia Panel 10 genes

- Surfactant dysfunction and respiratory distress in premature infants Panel 8 genesSyndromic Autism Panel 83 genesVascular Disorders Panel 21 genes

+ X-Linked Intellectual Disability (XLID) Panel 114 genes

Whole exome sequencing analysis is available for trios and singletons. Custom panel and single gene requests are accepted. Contact the lab for more details.

MoleCular DiagnosTiC TesTing

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Syndrome Gene Sequencing Del/Dup Present in panel3-Methylcrotonyl-CoA Carboxylase Deficiency MCCC1, MCCC2 • •Aarskog syndrome FGD1 • • +Adrenoleukodystrophy, X-linked ABCD1 • • +Allan-Herndon-Dudley syndrome SLC16A2/MCT8 • •Alpha-Mannosidosis MAN2B1 • • Aminoglycoside-induced Hearing Loss MTRNR1 • •Angelman syndrome: Methylation analysis, UBE3A Sequencing and Deletion/Duplication, UPD15 analysisARX-related spectrum ARX • • +Aspartylglucosaminuria AGA • •Atypical Rett syndrome CDKL5 • • +ATRX syndrome ATRX • • +Batten Disease, Neuronal Ceroid Lipofuscinosis 3 CLN3 • • Beckwith Wiedemann syndrome Methylation •Beta-Mannosidosis MANBA • •Biotinidase deficiency BTD • •Borjeson-Forssman-Lehmann syndrome PHF6 • • +Cardio-Facio-Cutaneous (CFC) syndrome Tier 1 BRAF • Tier 2 MAP2K1, MAP2K2 • Tier 3 KRAS • Carnitine Palmitoyltransferase Deficiency 1A CPT1A • •Carnitine Palmitoyltransferase II Deficiency CPT2 • •CASK-related Intellectual Disability CASK • • +CHARGE syndrome CHD7 • • Christianson syndrome (Angelman-like syndrome) SLC9A6 • • +Citrullinemia Type I ASS1 • •

Coffin-Lowry syndrome RPS6KA3 • • +Congenital Disorder of Glycosylation, Ia PMM2 • •Congenital Disorder of Glycosylation, Ib MPI • •Congenital Disorder of Glycosylation, Ic ALG6 • •Congenital Rett Variant FOXG1 • • Connexin 26 GJB2 • • Cornelia de Lange Syndrome NIPBL, SMC1A, RAD21, SMC3, or HDAC8 +

Costello syndrome • • Tier 1 (First Coding Exon) HRAS • • Tier 2 (Remaining Exons) HRAS • • Cystic Fybrosis CTFR • • +Creatine Transporter Deficiency SLC6A8 • • +DCX-related spectrum DCX • • +Duchenne/Becker Muscular Dystrophy DMD • +Early Infantile Epileptic Encephalopathy 4 STXBP1 • • Ectrodactyly, Ectodermal Dysplasia, Clefting syndrome TP63/p63 • •Fabry Disease GLA • FG syndrome MED12 • • +FGFR2-related disorders FGFR2 • •

MoleCular DiagnosTiC TesTing ConT..

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Syndrome Gene Sequencing Del/Dup Present in panel

FGFR3 -related disorders (selected exons) FGFR3 • FLNA – related disorders FLNA • • +Fragile X syndrome FMR1 Triplet Repeat Analysis +

FRAXE syndrome AFF2 Triplet Repeat Analysis +Fucosidosis FUCA1 • •Galactosemia, classic GALT • •Galactosialidosis CTSA • • Gaucher Disease GBA • • Glutaric Acidemia, Type I GCDH • •Greig cephalopolysyndactyly syndrome GLI3 • •Glycogen Synthase Deficiency GYS2 •GM1 Gangliosidosis GLB1 • • Hemochromatosis - Targeted Mutation Analysis HFEHay-Wells syndrome TP63/p63 • •Hunter syndrome, MPS II IDS • • +Hurler, Hurler-Scheie, and Scheie syndrome, MPS I IDUA • • Isolated Split-Hand/Foot TP63/p63 • •Kabuki syndrome MLL2 • • Krabbe Disease GALC • •Leopard Syndrome Tier 1 PTPN11 • Tier 2 RAF Sequencing of exons 7, 14 & 17 Tier 3 BRAF • Lujan-Fryns syndrome MED12 • • Marfan syndrome FBN1 • • Maroteaux-Lamy syndrome, MPS VI ARSB • •MCAD ACADM • •Metachromatic Leukodystrophy ARSA • •Morquio syndrome, type A, MPS IVA GALNS • • Morquio syndrome, type B, MPS IVB GLB1 • • Mucolipidosis II/IIIA GNPTAB/GNPTG • • Myotonic Dystrophy DM1 Triplet Repeat AnalysisMyotubular Myopathy, X-linked MTM1 • • +Neuronal Ceroid Lipofuscinosis type 1 PPT1 • • Neuronal Ceroid Lipofuscinosis type 2 TPP1 • • Niemann-Pick Disease A/B (Acid sphingomyelinase) SMPD1 • •

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Syndrome Gene Sequencing Del/Dup Present in panel

Noonan syndrome Tier 1 PTPN11 • • Tier 2 SOS1 • • Tier 3 RAF1, KRAS Sequencing & SHOC2 – p.S2G Tier4 BRAF, MAP2K1, NRAS OPHN1-related X-linked Intellectual Disability OPHN1 • • +Ornithine transcarbamylase deficiency OTC • • +Pelizaeus-Merzbacher Disease, Spastic paraplegia 2 PLP1 • • +Phenylketonuria PAH • •Pitt-Hopkins syndrome TCF4 • • POLG1 – related disorders POLG1 • • Pompe Disease GAA • • Prader-Willi syndrome UPD 15 & methylation • •PTEN –related Disorders PTEN • • Renpenning syndrome PQBP1 • • +Rett syndrome MECP2 • • +Russell Silver syndrome UPD 7 & 11p15.5 related methylation •Sandhoff Disease HEXB • •Saethre-Chotzen syndrome TWIST1 • •Sanfilippo syndrome Type A, MPS IIIA SGSH • •Sanfilippo syndrome Type B, MPS IIIB NAGLU • •Sanfilippo syndrome Type C, MPS IIIC HGSNAT • •Sanfilippo syndrome Type D, MPS IIID GNS • •Short-Chain Acyl-CoA Dehydrogenase (SCAD) ACADS • •Sialidosis NEU1 • •Simpson-Golabi-Behmel syndrome type 1 GPC3 • • +Sly syndrome, MPS VII GUSB • • Sotos syndrome NSD1 • • Tay-Sachs Disease HEXA •Succinyl CoA:3-oxoacid CoA transferase (SCOT) OXCT1 • •Thrombosis Panel: Factor V Leiden & Prothrombin Targeted Mutation AnalysisUniparental disomy Chromosomes 7, 14, 15 VLCAD Deficiency ACADVL • •X-inactivation analysis X-linked, Female Limited Epilepsy with ID PCDH19 • • +X-linked Hydrocephalus L1CAM • • +X-linked Opitz G/BBB syndrome MID1 • • +

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enzyMe Panels

Dried Blood Spot Lysosomal Enzyme PanelAlpha-mannosidosis, Aspartylglucosaminuri, Beta-mannosidosis, Fabry Disease, Fucosidosis, Gaucher disease, GM1 Gangliosidosis/Morquio type B (MPS IVB), Hunter syndrome (MPS II), Hurler syndrome (MPS I), Krabbe Disease, Niemann-Pick A/B, Pompe disease, Sanfilippo syndrome type B (MPS IIIB), Schindler/Kanzaki Disease, Tay Sachs/Sandhoff Disease

Hydrops Panel Galactosialidosis, Gaucher Disease, GM 1 gangliosidosis, Sialidosis, Sly syndrome, MPS VII

Lysosomal Storage Disease PanelAlpha-Mannosidosis, Aspartylglucosaminuria, Beta-Mannosidosis,Fabry Disease, Fucosidosis, Gaucher Disease, GM 1 gangliosidosis/ Morquio type B (MPS IVB), Hurler syndrome; MPS I, Krabbe Disease, Metachromatic Leukodystrophy, Niemann-Pick A/B, Schindler/ Kanzaki Disease, Tay Sachs/Sandhoff Disease

Morquio syndrome Panel, MPS IV Morquio type A & Morquio type B

Mucopolysaccharidosis (MPS) Enzyme Panel Hurler syndrome (MPS I), Hunter syndrome (MPS II), Sanfilippo syndrome; Type A (MPS IIIA), Type B (MPS IIIB), Type C (MPS IIIIC), & Type D (MPS IIID), Morquio syndrome; Type A (MPS IVA), Type B (MPS IVB), Maroteaux-Lamy syndrome (MPS VI), Sly syndrome (MPS VII)

Multiple Sulfatase Deficiency Panel Arylsulfatase B, Iduronate-2-sulfatase, and N-acetyl-galactosamine-6-sulfatase

Neurological (Sphingolipidoses) PanelFabry disease, Gaucher Disease, GM1 gangliosidosis, Krabbe Disease, Metachromatic Leukodystrophy, Neuronal Ceroid Lipofuscinosis 1, Neuronal Ceroid Lipofuscinosis 2( Simplify to 1 & 2?), Niemann-Pick A/B, Tay Sachs/Sandhoff Disease

Sanfilippo syndrome Panel, MPS IIISanfilippo syndrome, Types A, B, C and D (MPS IIIA, IIIB, IIIC, and IIID)

Oligosaccharidoses PanelAlpha-Mannosidosis, Aspartylglucosaminuria, Beta-Mannosidosis, Fucosidosis, GM1 gangliosidosis, Schindler/Kanzaki Disease,Sialidase only if fibroblasts are submitted

bioCheMiCal DiagnosTiC TesTing

bioCheMiCal analyTes PlasMa urine Csf seruM

Acylcarnitine profileAmino acids • • •Carnitine, total and free • •Creatine/GAA • •Creatine Kinase •Galactose-1-phosphate (RBC) Glutarylcarnitine (C5-DC) •Glycosaminoglycans, total quantitative •Homocysteine •Oligosaccharide Analysis via LC-MS/MS •Organic acids •Orotic acid •Sialic acid •Transferrin isoelectric focusing (CDG screening) •Tryptophan •

MPS Analysis includes quantitative HS/DS/CS/KS & total GAGs •

Biochemical Genetics Profile: amino acids, acylcarnitine profile, carnitine, & organic acids

Storage Disease Screening Panel: Includes: MPS analysis (quantitative HS/DS/CS/KS & GAGs) Oligosaccharide analysis, and Sialic Acid, total and free

urine MuCoPolysaCChariDosis MoniToring

Total GAGs DS HS KS CS

MPS I/II • • •MPS III • •MPS IV • • •MPS VI • •MPS VII • • •

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Morquio, type B β-galactosidaseMucolipidosis II / III Plasma screenNeuronal Ceroid Lipofuscinosis 1 Palmitoyl-protein thioesterase 1Neuronal Ceroid Lipofuscinosis 2 Tripeptidyl peptidase 1Niemann-Pick A/B Acid sphingomyelinase Pompe Disease (Glycogen Storage Disease Type II) α-1,4-glucosidaseSanfilippo A Heparan-N- sulfataseSanfilippo B N-acetyl-α-glucosaminidaseSanfilippo C Acetyl CoA:glucosamine N-acetyltransferase Sanfilippo D N-acetyl glucosamine-6-sulfataseSchindler/Kanzaki Disease N-acetyl alpha galactosaminidaseSialidosis α-neuraminidase, sialidase Sly syndrome, MPS VII β-glucuronidaseTay Sachs/Sandhoff Disease β-hexosaminidase

Alpha-mannosidosis α-mannosidase Aspartylglucosaminuria AspartylglucosaminidaseBeta-mannosidosis β-mannosidaseBiotinidase biotinidase deficiencyFabry disease α-galactosidaseFucosidosis α-fucosidase Gaucher Disease β-glucosidase GM1 Gangliosidosis β-galactosidase Hunter syndrome, MPS II iduronate-2-sulfataseHurler syndrome, MPS I α-iduronidaseKrabbe Disease galactocerebrosidaseMaroteaux Lamy syndrome, MPS VI arylsulfatase BMetachromatic leukodystrophy arylsulfatase AMorquio, type A N-acetyl-galactosamine-6-sulfatase

inDiviDual enzyMes

fish for CongeniTal abberaTions

Disorder ChromosomeAndrogen Receptor Xq12

Angelman syndrome 15q11q13Autism dup15q12Cri-du-chat syndrome 5p-DiGeorge/VCF 22q11.2Kallmann syndrome Xp22.3Miller-Dieker syndrome 17p13Phelan-McDermid syndrome 22q13.3 Prader-Willi syndrome 15q11q13

Smith Magenis syndrome 17p11.2Sex Reversal/Ambiguous Genitalia Panel

includes SRY/Xcen & X/Y dual assay probes

Steroid Sulfatase Deficiency (STS)/X-linked Icthyosis

Xp22.3

Trisomy screen 13, 18, 21, X, YWilliams syndrome 7q11.23

Wolf-Hirschhorn syndrome 4p-X/Y dual assay x,y

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• Routine blood • High resolution

-Whole Genome SNP Microarrays CytoScan® Dx Assay (FDA Cleared array)* *Can only be ordered for certain indications: • developmental delay • intellectual disability • congenital anomalies • dysmorphic features CytoScan HD Array-Custom Exon Array (725 genes) Can be ordered as single gene, two genes, group of genes, or full array for all genes

MiCroarray

CyTogeneTiC DiagnosTiC TesTing

onCology MuTaTion analysis

AML(FLT3-ITD, & FLT3-TKD mutations; NPM1 Codon 12

Lung AdenocarcinomaEGFR amplificaiton and mutation analysisBRAF mutation (V600E)PTEN mutatin analysisLung Adenocarcinoma panel (includes EGFR amplification mutation analysis, BRAF & PTEN mutation analysis

Brain TumorIDH1 R132H mutation1p/19q co-deletionNEK1 deletionTP53 deletionCDKN2A/CDKN28 deletionEGFR AmplificationPTEN deletionNF1 deletionAdult Brain Tumor Panel (includes 98 genes listed

MelanomaBRAF mutation analysis (V600E & V600K)Melanoma Array (Includes genomic gains, losses, and loss of heterozygosity

ChroMosoMe analysis

-Acute Lymphocytic Leukemia (ALL) Array-Acute Myelocytic Leukemia (AML) Array-Chronic Lymphocytic Leukemia (CLL) Array-Chronic Myelocytic Leukemia (CML) Array -OncoScan Microarray (any FFPE tumor Tissue)-Pregnancy Loss/POC Microarray-Prenatal Whole Genome SNP Microarray-Targeted Infertility Microarray-X-Chromosome CGH Microarray 105K

• Amniotic fluid • CVS

• Rule out mosaicism• Solid tissue

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Bone Marrow chromosome

Stimulated/Unstimulated blood

heMaTologiCal anD onCologiCal Disease sTuDies

FISH Panels & Specific Probes

MYC (2p24.1) D7S486 (7q31) MLL (11q3) TOP2A (17q21)

ALK (2p23) C-MYC (8q24) ETV6/TEL (12p13) SYT (18q11.2)

BCL6 (3q27) p16 (9p21) Retinoblastoma (RB1) MALT1 (18q21)

CSF1R (5q33-q34) 9q34 D13S319 (13q14) BCL2 (18q21)

EGR-I (5q31) PTEN (10q23) IgH (14q32) D20S108 (20q12)

MYB (6q23) Cyclin D1/CCND1 (11q13) CBFB (inv16) 20q13

EGFR (7p12) ATM (11q22.3) p53 (17p13.1) EWSR1 (22q12)

inDiviDual Probes

(Interphase and/or Metaphase)

fish heMaTology Panels

Acute Lymphocytic Leukemia

Acute Myelocytic Leukemia

Acute Promyelocytic Leukemia

Chronic Lymphocytic Leukemia

Chronic Myelocytic Leukemia

Chronic Myelomonocytic Leukemia

Multiple Myeloma

Myelodysplastic States

Non-Hodgkins Lymphoma

Pediatric Acute Lymphoblastic Leukemia

Reflex Panel for IgH breakapart Includes t(8;14), t(14;18), t(11;14)

Mission StatementThe Greenwood Genetic Center is a nonprofit institute organized to provide clinical genetic

services and laboratory testing, to develop educational programs and materials, and to conduct research in the field of medical genetics.

106 Gregor Mendel Circle • Greenwood, SC 29646

(800) 473-9411Fax (864) 941-8141

@ggc.org