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Home , Barbara McClintock, Chromosome 11, COX8A, Cytogenetics, Dicentric chromosome, Karyotype

Cytogenetics: Nomenclature and Disease

Willis Navarro, MD Medical Director, Transplant Services National Marrow Donor Program Overview

• Normal – Structure – • Chromosomal Disruptions – Types ofCf Chromosomal C hanges • Disruptions and Disease Structural Overview • DNA forms a double helix • Double helix structure is wound around • DNA/ complex then forms th e structure

http://ghr.nlm.nih.gov/handbook/illustrations/chromosomestructure Division and

• Tissue cells of interest are grown in culture • Cell must be “frozen” at methtaphase – Mitotic inhibitor added – Chromosomes condensed – Cells harvested

From: http://www.google.com/imgres?imgurl=http://nte-serveur.univ-lyon1.fr/nte/EMBRYON/www.uoguelph.ca//devobio/miller/mitosis1.gif&imgrefurl=http://nte-serveur.univ- lyon1.fr/nte/EMBRYON/www.uoguelph.ca/zoology/devobio/210labs/mitosis1.html&h=538&w=450&sz=24&tbnid=PXVEm8paeVwJ::&tbnh=132&tbnw=110&prev=/images%3Fq%3Dmitosis&hl =en&usg=__XTdVA_DgEhY6qk-d9HDMvHcVN9Q=&sa=X&oi=image_result&resnum=4&ct=image&cd=1 Chromosome Basics

C metacentric

submetacentric C

C

Acrocentric

From: http://www.miscarriage.com.au/images/pages/karyotype_normal.jpg

• 22 pairs plus 2 sex chromosomes (diploid number: 46): (46, XX) • Composed of DNA plus infrastructure (histones, , RNA, sugars) • 3 groups of shapes based on position, arm length Example of G-Banding:

• GTL stain: Giemsa//Leishman p arm • Chr 11 is submetacentric • RttiidRepresentative ideogram Centromere • Stained to distinguish denser and less dense areas • Unique patterns for each chromosome q arm • Many genes coded • Banding ≠ genes

From: http://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Chromosome_11.svg/164px-Chromosome_11.svg.png How Do You Define a ?

• DNA sequence begins with a start codon; ends with a stop codon • Amino acids (each with a 3-character code) then join to form a which then has a function • There i s “fill er ” DNA that codes for other stuff So Many Genes…

• ARHGAP20 109952.97611q23.2ARHGEF12 119713.15611q23.3ATM 107598.76911q22-q23BAD 63793.87811q13.1BIRC3 101693.40411q22C11orf30 75833.71711q13.5CARS 2978.73511p15.5CASP1 104401.44711q23CBL 118582.20011q23.3-qterCCND1 69165.05411q13CHKA 67576.90211q13.1DDB2 47193.06911p12-p11DDX10 108041.02611q22-q23EXT2 44073.67511p12-p11FANCF 22600.65511p15HRAS 522.24211p15.5KAT5 65236.06511q13LMO2 33836.69911p13MAML2 95351.08811q21MEN1 64327. 57011q13MIRN125B1 121475. 67511MLL 117812. 41511q23MRE11A 93790. 11511q21MYEOV parmp arm 68818.19811q13.2NUMA1 71391.55911q13NUP98 3689.63511p15PAK1 76710.70811q13-q14PICALM 85346.13311q14POU2AF1 110728.19011q23.1RELA 65178.39311q13RSF1 77054.92211q13.5SDHD 111462.83211q23SPA17 124048.95011q24.2SPI1 47332.98511p12-p11.22WT1 32365.90111p13ZBTB16 113436.49811q23 ACAT1 107497.46811q22.3ACP2 47217.42911p11.2ADAMTS15 129824.07911q25ADAMTS8 129780.02811q25ADM 10283.21811ADRBK1 66790.48111q13AHNAK 62039.95011q12-q13AIP 67007.09711q13.3ALDH3B2 67186.20911q13ALKBH3 43858.97311p11.2ALKBH8 106880.54411q22.3AMPD3 10428.80011p15ANKK1 112763.72311q23.2ANO1 69602.05611q13.2APBB1 6372.93111p15API5 43290.10911APLNR 56757.64311q12APOA1 116211.67911q23-q24ARAP1 Centromere 72073.76211q13.3ARCN1 117948.32111q23.3ARFIP2 6453.50211p15ARHGAP1 46655. 20811p11. 2ARHGEF17 72697. 31711q13. 3ARL2 64538. 16211q13ARRB1 74654. 13011q13ART1 3622.93711p15ASCL2 2246.30411p15.5B3GAT1 133753.60811q25B3GNT6 76423.08311q13.4BARX2 128751.09111q24.3BCL9L 118272.06111q23.3BDNF 27633.01811p14.1BIRC2 101723.17611q22BRMS1 65861.38011q13-q13.2BRSK2 1367.70511p15.5BTG4 110843.46611q23C11orf17 8889.27711p15.3C11orf68 65440.85911q13.1C1QTNF4 47567.79211q11C1QTNF5 118714.86211q23.3CADM1 114549.55511q23.2CALCA 14946.62411p15.2CAPN1 64705.91911q13CASP4 104318.80411q22.2- q22.3CASP5 104370.17211q22.2-q22.3CAT 34417.05411p13CCDC73 32580.20211p13CCKBR 6237.54211p15.4CD151 822.95211p15.5CD248 65838.53411q13CD3E 117680.50511q23CD44 35116.99311p13CD5 60626.50611q13CD59 33681.13211p13CD6 60495.69111q12.2CD81 2355.12311pter- p11.2CD82 44543.71711p11.2CDC42EP2 64838.90711q13CDK2AP2 67030.54411q13CDKN1C 2861. 02411p15. 5CDON 125331. 92311q23-q24CENTD2 72073. 76211q13. 3CEP57 95163. 29011q21CFL1 qarmq arm 65378.86111q13.1CHEK1 125000.24611q24.2CHORDC1 89574.26511q14.3CHRDL2 74085.12211CKAP5 46721.66011p11.2CLCF1 66888.21511q13.3CLP1 57181.20611q12CNTF 58146.72111q12CNTN5 98397.08111q21-q22.2COP1 104417.263-COX8A 63498.65511q12-q13CPT1A 68278.66411q13.2CREB3L1 46255.80411q11CRTAM 122214.46511q24.1CRY2 45825.24511p11.2CRYAB 111284.56011q22.3-q23.1CST6 65536.03811q13CTNND1 57285.81011q12.1CTSD 1730.56111p15.5CTSF 66087.51111q13.2CTTN 69922.26011q13CUL5 107384.61811q22.3CXCR5 118259.75111q23.3CYB5R2 7642.90211p15.4DCPS 125678.85711q24DDB1 60823.49511q12-q13DDX25 125279.48211q24DDX6 118123.68311q23.3DEAF1 634.22511p15.5DGKZ 46339.72111p11.2DKK3 11941.11911p15.3DLAT 111400.74811q23.1DNAJC4 63754.32911q13DPF2 64857.92211q13.1DPP3 66004.45611q12-q13.1DRD2 112785.52711q23DUSP8 15311531.857.85711p1511p15.5.5DYNC2H1 102485102485.370.37011q21-q22q22.1.1EED 8563385633.463.46311q1411q14.2.2-q22q22.3.3EHF 3459934599.244.24411p12EI24 124944.50811q23EIF3F 7965.44311p15.4EIF4G2 10775.16911p15ELF5 34456.91811p13-p12ESRRA 63829.62011q12ETS1 127833.87011q23.3F2 46697.31911p11-q12FADD 69726.91711q13.3FADS2 61352.28911q12.2FAM111B 58631.28611q12.1FAM89B 65096.39611q23FAT3 91724.91011q14.3FAU 64644.67811q13FBXL11 66644.07411q13.1FCHSD2 72225.43811q13.3FEN1 61316.72611q12FEZ1 124820.85811q24.2FGF19 69222.18711q13.1FGF3 69333.91711q13FGF4 69296.97811q13.3FLI1 128069.02311q24.1-q24.3FLRT1 63627.93811q12-q13FOLH1 49124.76311p11.2FOLR1 71578.60711q13.3- q14.1FOLR2 71605.46711q13.3-q14.1FOSL1 65416.26811q13FOXR1 118347.62711q23.3FRAG1 Dessen P, Knuutila S, Huret JL Chromosome 11. Atlas Genet Cytogenet 3786.36011p15.5FSHB 30209.13911p13FTH1 61488.33311q13FUT4 93916.77511q12-qterFXC1 Oncol Haematol. 2002. 6459.25311p15.2-q15.5FZD4 86334.36911q14-q21GAB2 77603.99011q14.1GAL 68208.55911q13.2GAS2 22652.93111p14.3GCRG224 82211.05611q13-q14GNG3 62231.70911p11GRM5 87880.62611q14.3GSTP1 URL : http://AtlasGeneticsOncology.org/Indexbychrom/idxa_11.html 67107.64211q13-qterGTF2H1 18300.71911p15.1-p14H19 1972.98311p15.5H2AFX 118469.79511q23.3HBB © Atlas of and Cytogenetics in and Haematology 5203.27211p15.5HCCA2 1447.26911p15.5HEPACAM 124294.35611q24.2HEPN1 124294.356-HIPK3 33235.74411p13HPS5 18256.79311p14HRASLS2 63076.81811q12.2HRASLS3 63098.52011q12.3HSPA8 122433.41011q24.1HSPB2 111288.70911q22-q23HTATIP2 20341.86511HTR3A 113351.12011q23.1- q23.2HYOU1 118420.10611q23.1-q23.3ICEBERG 104513.87911q21-q22IFITM1 303.99111p15.5IFITM3 309.67311p15.5IGF2 2106.92311p15.5IGF2AS 2118.31311p15.5IGHMBP2 68427.89511q13.3IL10RA 117362.31911q23IL18 111519.18611q22.2-q22.3ILK 1132.47411p15.5MUC5B 1200.87211p15.5MUC6 1002.82411p15.5MUS81 65384.44811q13MYOD1 17697.68611p15NAALAD2 89507.46611q14.3-q21NAP1L4 … What can go wrong with a gene?

• The correct sequence is critical to coding the right protein/protein structure • If the chromosome carrying a particular gene is altered, then the resulting mutated protein or control elements may cause problems What can go wrong with a ch?hromosome? • Constitutional vs acquired abnormalities

• Numerical abnormalities – : loss of a whole chromosome – : gain of a whole chromosome

• Structural abnormalities – Deletions – Inversions – Translocations Monosomy X: CiilLConstitutional Loss Trisomy 21: CCiilGionstitutional Gain

http://ghr.nlm.nih.gov/handbook/illustrations Deletion 5q AidLAcquired Loss • Interstitial losses of the long arm of • These losses resu lt in large numbers of genes being lost • Often associated with myelodysplastic syndromes and acute

myeloid From: http://atlasgeneticsoncology.org/Educ/Images/GeneticCancerFig7.jpg Inversions

http://ghr.nlm.nih.gov/handbook/illustrations Inversion (3)(q24q27) AAidAblicquired Abnormality

From: http://members.aol.com/chrominfo/images/inv3ideo.gif • Int erstiti al segment i nvert s Translocations

http://ghr.nlm.nih.gov/handbook/illustrations Translocation t(9;22) AidAbliAcquired Abnormality • Material is exchanged between chromosomes 9 and 22, creating a new : bcr/ • Breakpoint may vary a bit such that the newly created fusion protein may be of several lengths – p190 (kDa) From: http://members.aol.com/chrominfo/images/inv3ideo.gif – p210

http://atlasgeneticsoncology.org/Anomalies/CML.html

http://ghr.nlm.nih.gov/handbook/illustrations

http://ghr.nlm.nih.gov/handbook/illustrations Ring Chromosomes

http://ghr.nlm.nih.gov/handbook/illustrations Duplication

http://ghr.nlm.nih.gov/handbook/illustrations Recap of Basic Abnormalities

• Loss or gain of entire chromosomes – Monosomy –Trisomy • Structural – Deletions – IiInversions – Translocations • Plus more uncommon types of abnormalities – Derivative chromosome (der) • Used when only one chromosome of a translocation is present or • One chromosome has two or more structural abnormalities – Dicentric chromosome (dic) [chromosome has two ] – Duplicate (dup) [duplication of a portion of a chromosome] – Insertion (ins) – Isochromosomes (i) [both arms are the same] – (mar) [unidentifiable piece of chromosome] – (r) – Hyperdiploidy: greater than 48 chromosomes Interpreting Cytogenetic Reporting

•In sequence: – the overall number of chromosomes identified – sex chromosomes – affected chromosomes – type of abnormalities described in shorthand – chromosomal band location – In brackets, the number of cells with a given • Examples – 46, XX; t(9;22)(q13;q22) [20] – 47, XY; +21 [12] – 46, XX; inv 16(q13; q21) [20] – 45, XY; -5 [18]; 46, XY [2] – 46, XY; -5 (q13) [4]; 46, XX [16] Cytogenetic Pioneers Barbara McClintock – First geneti c map of mai ze – Genetic and physical characteristics correlated – Her work helped explain how cells that share the same can hdifftftihave different functions – for transposons in 1983

Janet Rowley – Hypothesized that might contain non-random genetic abnormalities – 1972: Showed that recurring chromosomal abnormalities occurred in leukemia and sometimes defined the disease’s characteristics Leukemias and Cytogenetics

• Certain morphologic subtypes were known to have distinct prognoses and/or clinical syndromes (M0-M7) • Examples: – acute ppyyromyelocytic leukemia ()(M3) • High bleeding risk due to coagulopathy but favorable prognosis • t(15; 17)(q22;q12) – AML, subtype M4eo • Favorable prognosis • inv(16)(p13;q22) – Chronic myeloid leukemia •t(9 ;22)(q 11 ;q34 ) – Some myelodysplastic patients— typically older women--had a pattern of normal platelet counts and a favorable prognosis • 5q- syndrome Risk Stratification for Acute LkLeukem ias UiCUsing Cytogenet ics • Previous to and others’ observations about cytogenetics and prognosis, leukemias were only categorized by morphology under the

•AML – Favorable Risk • inv (16) • t (8;21) • t (15;17) – Intermediate Risk • All abnormalities not in favorable or high risk categories, plus normal – Poor Risk • Monosomy 5 or 7; 5q-; 7q- • t (9;22) • Complex (3 or more abnormalities) •ALL – Favorable risk • Hyperdiploidy – High Risk • t (1;19) • t (9;22) • t (4;11) Pre-TED Form (1): Cyto data

• First three AML cyto abnormalities are associated with favorable prognosis (AML/ETO, e.g., refers to the two genes involved in the leukemia) • AML with 11q23: often associated with previous topoisomerase inhib.-based chemotherapy (MLL gene is located at 11q23); usually t(9;11) (p22;q23) Pre-TED Form (2)

• IthIn the pre-TED exampl e a bove, Ph+ re fers to the cytogenetics; bcr refers to the detection of bcr/abl gene product, usually by PCR or FISH Form 2100 Chimerism Studies

• No te tha t f or coll ec tion o f chimerism data, PCR is not an option and should not be recorded under “other” Disease Status: FISH

• For data purposes, FISH is a subset of cytogenetics (cellular level) • Molecular evidence would be PCR and similar The Future of Prognosticating Outcomes in Acute Leukemia • May be based on the molecular of the leukemia as ascertained by –PCR –FISH – Microarray data/gene profiling • More and more critical to understand the molecular basis as more targeted therapies bilblbecome available – Anti-bcr/abl drugs: imatinib and 2nd generation drugs – Anti flt3 etc. Summary

• A variety of chromosomal abnormalities can be characterized and described using cytogenetics • Non-random chromosomal alterations occur, can define the disease (e.g. APML), and can have important prognostic value • Not all genetic abnormalities can be seen using cytogenetic techniques (e. g. normal cytogenetics in AML) • Newer techniques (polymerase chain reaction [PCR], fluorescen t i n-situ hy br idiza tion [FISH]) can assist in searching for occult genetic aberrations Web References

• http://www.slh.wisc.edu/wps/wcm/connect/e xtt/tti/tranet/cytogenetics/ • http://ghr.nlm.nih.gov/handbook/illustrations