Cytogenetic Biochemical

Transcription

1 Diagnostic Laboratories Test Menu Molecular Cytogenetic Biochemical

2 Table of Contents Lab Directors & Genetic Counselors...2 Molecular Diagnostic Lab Next Generation Sequencing Panels...3 Biochemical Diagnostic Lab Enzyme Panels...7 Individual Enzymes...8 Analytes...8 Monitoring Tests...8 Cytogenetic 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

3 Lab Directors Mike Friez, PhD, FACMG Director of Diagnostic Labs Molecular Biochemical Cytogenetic Jennifer A. Lee, PhD, FACMG Lead Molecular Director Tim Wood, PhD, FACMG Director Barbara DuPont, PhD, FACMG Senior Director Fatima Abidi, PhD Technical Director Laura Pollard, PhD, FACMG Associate Director Alka Chaubey, PhD, FACMG Director Julie R Jones, PhD, FACMG Director of Clinical Genomics Sequencing Program Taraka Donti, PhD Assistant Director Genetic Counselors Robin Fletcher, MS, CGC Laboratory Genetic Counselor Kellie Walden, MS, CGC Laboratory Genetic Counselor -2-

4 Molecular Diagnostic Testing Next Generation Sequencing Aortic Dysfunction or Dilation and Related Disorders Panel 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 Cornelia de Lange Panel Craniosynostosis Panel Dilated Cardiomyopathy (DCM)/Arrhythmogenic Cardiomyopathy Panel Epilepsy/Seizure Panel Hearing Loss Panel 35 genes 5 genes 8 genes 51 genes 145 genes 91 genes - Hermansky-Pudlak Syndrome and Pulmonary Fibrosis Panel 25 genes Hypertrophic 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 Non-immune Hydrops Panel 9 genes 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 Rhabdomyolysis and Metabolic Myopathies Panel Skeletal Dysplasia Panel 21 genes 47 genes 10 genes - Surfactant dysfunction and respiratory distress in premature infants Panel 8 genes Syndromic Autism Panel Vascular Disorders Panel 83 genes 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.

5 Syndrome Gene Sequencing Del/Dup Present in panel 3-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 analysis ARX-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 FGFR2-4-

6 Molecular Diagnostic Testing Cont.. 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 HFE Hay-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 Analysis Myotubular Myopathy, X-linked MTM1 + Neuronal Ceroid Lipofuscinosis type 1 PPT1 Neuronal Ceroid Lipofuscinosis type 2 TPP1 Niemann-Pick Disease A/B (Acid sphingomyelinase) SMPD1-5-

7 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 Analysis Uniparental 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 MID

8 Biochemical Diagnostic Testing Enzyme Panels Dried Blood Spot Lysosomal Enzyme Panel Alpha-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 Panel Alpha-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) Panel Fabry 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 III Sanfilippo syndrome, Types A, B, C and D (MPS IIIA, IIIB, IIIC, and IIID) Oligosaccharidoses Panel Alpha-Mannosidosis, Aspartylglucosaminuria, Beta-Mannosidosis, Fucosidosis, GM1 gangliosidosis, Schindler/Kanzaki Disease, Sialidase only if fibroblasts are submitted -7-

9 Individual Enzymes Alpha-mannosidosis α-mannosidase Aspartylglucosaminuria Aspartylglucosaminidase Beta-mannosidosis β-mannosidase Biotinidase biotinidase deficiency Fabry disease α-galactosidase Fucosidosis α-fucosidase Gaucher Disease β-glucosidase GM1 Gangliosidosis β-galactosidase Hunter syndrome, MPS II iduronate-2-sulfatase Hurler syndrome, MPS I α-iduronidase Krabbe Disease galactocerebrosidase Maroteaux Lamy syndrome, MPS VI arylsulfatase B Metachromatic leukodystrophy arylsulfatase A Morquio, type A N-acetyl-galactosamine-6-sulfatase Morquio, type B β-galactosidase Mucolipidosis II / III Plasma screen Neuronal Ceroid Lipofuscinosis 1 Palmitoyl-protein thioesterase 1 Neuronal Ceroid Lipofuscinosis 2 Tripeptidyl peptidase 1 Niemann-Pick A/B Acid sphingomyelinase Pompe Disease (Glycogen Storage Disease Type II) α-1,4-glucosidase Sanfilippo A Heparan-N- sulfatase Sanfilippo B N-acetyl-α-glucosaminidase Sanfilippo C Acetyl CoA:glucosamine N-acetyltransferase Sanfilippo D N-acetyl glucosamine-6-sulfatase Schindler/Kanzaki Disease N-acetyl alpha galactosaminidase Sialidosis α-neuraminidase, sialidase Sly syndrome, MPS VII β-glucuronidase Tay Sachs/Sandhoff Disease β-hexosaminidase Biochemical Analytes Plasma Urine CSF Serum Acylcarnitine profile Amino 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 -8-

10 Cytogenetic Diagnostic Testing Microarray -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 -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 Chromosome Analysis Routine blood High resolution Rule out mosaicism Solid tissue Amniotic fluid CVS Oncology Mutation Analysis AML (FLT3-ITD, & FLT3-TKD mutations; NPM1 Codon 12 Lung Adenocarcinoma EGFR amplificaiton and mutation analysis BRAF mutation (V600E) PTEN mutatin analysis Lung Adenocarcinoma panel (includes EGFR amplification mutation analysis, BRAF & PTEN mutation analysis Brain Tumor IDH1 R132H mutation 1p/19q co-deletion NEK1 deletion TP53 deletion CDKN2A/CDKN28 deletion EGFR Amplification PTEN deletion NF1 deletion Adult Brain Tumor Panel (includes 98 genes listed Melanoma BRAF mutation analysis (V600E & V600K) Melanoma Array (Includes genomic gains, losses, and loss of heterozygosity Fish for Congenital Abberations Disorder Androgen Receptor Angelman syndrome Autism Chromosome Xq12 Cri-du-chat syndrome 5p- 15q11q13 dup15q12 DiGeorge/VCF 22q11.2 Kallmann syndrome Miller-Dieker syndrome Xp p13 Phelan-McDermid syndrome 22q13.3 Prader-Willi syndrome 15q11q13 Smith Magenis syndrome 17p11.2 Sex Reversal/Ambiguous Genitalia Panel Steroid Sulfatase Deficiency (STS)/X-linked Icthyosis Trisomy screen includes SRY/Xcen & X/Y dual assay probes Xp , 18, 21, X, Y Williams syndrome 7q11.23 X/Y dual assay x,y Wolf-Hirschhorn syndrome 4p- -9-

11 Hematological and Oncological Disease Studies FISH Panels & Specific Probes Bone Marrow chromosome Stimulated/Unstimulated blood 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) Individual Probes (Interphase and/or Metaphase) 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) -10-

12 @ ggc.org 106 Gregor Mendel Circle Greenwood, SC (800) Fax (864) Mission Statement The 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.