1. Published Standards for Molecular Laboratories Alexis B. Carter, MD, FCAP Director of Pathology Informatics Diplomate, American Board of Pathology, Molecular Genetic Pathology Department of Pathology and Laboratory Medicine Member, Center for Comprehensive Informatics

2. None in the last three years Financial Disclosures U.S. Requirement 18-Oct-10| IHTSDO - Toronto, Canada |2

3. Objectives Discuss international and some U.S. published standards for molecular pathology Provide fodder for discussion on standards for incorporation of molecular pathology terms into SNOMED CT 18-Oct-10| IHTSDO - Toronto, Canada |3

4. SNOMED CT SNOMED CT aims to improve patient care through the development of systems to accurately record health care encounters Molecular information is increasingly a part of health care encounters 18-Oct-10| IHTSDO - Toronto, Canada |4

5. Inclusions Published standards discussed will include – U.S. standards – International standards 18-Oct-10| IHTSDO - Toronto, Canada |5

6. Definition “Molecular Pathology” includes… Nucleic acid techniques (PCR, etc.) Chromosome analysis (Karyotyping) Fluorescence in situ hybridization (FISH) (and other ISH) Human Leukocyte Antigen (HLA) molecular testing 18-Oct-10| IHTSDO - Toronto, Canada |6

7. International Standards Nomenclature of gene names (HUGO) Nomenclature for sequence variations (HGVS) Nomenclature for factors of the HLA System (IMGT) International System for Human Cytogenetic Nomenclature 2009 (ISCN) 18-Oct-10| IHTSDO - Toronto, Canada |7

8. U.S. Standards Standards for categorizing sequence variations (ACMG) Report content standards (AMP, CAP) 18-Oct-10| IHTSDO - Toronto, Canada |8

9. Gaps in Standards Standard names for molecular methods Others? 18-Oct-10| IHTSDO - Toronto, Canada |9

10. HUGO Human Gene Nomenclature Committee (HGNC) – Guidelines first published 1979 – Updates 1987, 1995, 1997, 2002 – Includes Gene symbols, names, families and associated clinical disorders Homologies with other species How to name genes identified by sequence only How to reference gene rearrangements and recombinations – Refers nomenclature of associated enzymes and proteins to Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (http://ca.expasy.org/enzyme)http://ca.expasy.org/enzyme Wain HM, et al. Genomics. 2002;79(4):464-470. Wain HM, et al. Nucleic Acids Res. 2002;30(1):169-171. 18-Oct-10| IHTSDO - Toronto, Canada |10

11. HGVS Human Genome Variation Society http://www.hgvs.org/mutnomen/ Recommendations for nomenclature of sequence variations Example: Cystic Fibrosis 18-Oct-10| IHTSDO - Toronto, Canada |11 HistoricalHGVS NucleotideHGVS Amino Acid Delta F508c.1521-1523delCTTp.Phe508del den Dunnen JT, et al. Hum Mutat. 2000;15(1):7-12. Ogino S, et al. J Mol Diagn. 2007;9(1):1-6.

12. HGVS Gets rid of ambiguity surrounding nomenclature – Example of historical terminology: C36G – What does this mean? Is this cytosine to guanine at nucleotide 36? Is this DNA or RNA? Protein? Is this Cysteine to Glycine at amino acid 36? Unfortunately, not used much in medical literature 18-Oct-10| IHTSDO - Toronto, Canada |12

13. HLA Molecular Nomenclature IMGT/HLA database – http://imgt.cines.fr/ http://imgt.cines.fr/ – Official sequences for the WHO Nomenclature Committee For Factors of the HLA System – Part of the international ImMunoGeneTics project (IMGT) 18-Oct-10| IHTSDO - Toronto, Canada |13

14. HLA Molecular Nomenclature http://hla.alleles.org/nomenclature/nomencla ture_2009.html http://hla.alleles.org/nomenclature/nomencla ture_2009.html 18-Oct-10| IHTSDO - Toronto, Canada |14

15. ISCN 2009 International System for Human Cytogenetic Nomenclature – Chromosome analysis (karyotyping) – In situ hybridization (ISH) Specifically fluorescence in situ hybridization (FISH) – Comparative Genomic Hybridization (CGH) – Chromosome painting – Are introducing microarray nomenclature and nomenclature for Multiple Ligation-Dependent Probe Amplification (MLPA) 18-Oct-10| IHTSDO - Toronto, Canada |15

16. ISCN 2009 Multiple versions denoted by year of publication Most recent is 2009 Shaffer LG et al., eds. ISCN (2009): An International System for Human Cytogenetic Nomenclature. S. Karger: Basel 2009. 18-Oct-10| IHTSDO - Toronto, Canada |16

17. ACMG American College of Medical Genetics http://www.acmg.net Recommendations on reporting of sequence variations Updated 2008 18-Oct-10| IHTSDO - Toronto, Canada |17 Richards CS, et al. Genet Med. 2008;10(4):294-300.

18. ACMG Recommendations on reporting of sequence variations 1.Sequence variation is previously reported and is a recognized cause of the disorder 2.Sequence variation is previously unreported and is of the type which is expected to cause the disorder 3.Sequence variation is previously unreported and is of the type which may or may not be causative of the disorder 4.Sequence variation is previously unreported and is probably not causative of disease 5.Sequence variation is previously reported and is a recognized neutral variant 6.Sequence variation is not known or expected to be causative of disease, but is found to be associated with a clinical presentation 18-Oct-10| IHTSDO - Toronto, Canada |18 Richards CS, et al. Genet Med. 2008;10(4):294-300.

19. Reporting – Standards 18-Oct-10| IHTSDO - Toronto, Canada |19 Gulley ML, et al. Arch Pathol Lab Med. 2007;131(6):852-863.

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21. Reporting Standards Recommends use of HUGO-approved gene nomenclature Has some standards for approved use of method abbreviations – Q-PCR  Quantitative PCR – RT-PCR  Real-time PCR NOT reverse transcriptase PCR Recommends use of ACMG categories 18-Oct-10| IHTSDO - Toronto, Canada |21

22. Reporting Standards Has a number of other recommendations on nomenclature of genetic variation – Use of RefSeq through the National Library of Medicine in the U.S.A. http://www.ncbi.nlm.nih.gov/RefSeq – Use of Mutnomen HGVS nomenclature 18-Oct-10| IHTSDO - Toronto, Canada |22

23. Other Reporting Standards British Clinical Molecular Genetics Society (http://www.cmgs.org)http://www.cmgs.org Organisation for Economic Cooperation and Development (http://www.oecd.org)http://www.oecd.org Clinical and Laboratory Standards Institute (http://www.clsi.org)http://www.clsi.org 18-Oct-10| IHTSDO - Toronto, Canada |23

24. Gaps Nomenclature of Molecular Methods Plethora of result types Terminology can be confusing – Quantitative and qualitative – Homozygous, heterozygous, heteroplasmic, wild type – Multiplex assays generate multiple results (CF testing) – Deletion studies – Epigenetic results – High-throughput testing (microarrays) 18-Oct-10| IHTSDO - Toronto, Canada |24

25. Questions? 18-Oct-10| IHTSDO - Toronto, Canada |25