Cytogenetics: Nomenclature

and Disease
Willis Navarro, MD
Medical Director, Transplant Services
National Marrow Donor Program
 Overview
• Normal Chromosomes
– Structure
– Genes
• Chromosomal Disruptions
– Types off Chromosomal
C Changes
C
• Disruptions and Disease
 Structural Overview
• DNA forms a double
helix
• Double helix
structure is wound
around histones
• DNA/histone complex
th fforms the
then th
chromosome
structure

http://ghr.nlm.nih.gov/handbook/illustrations/chromosomestructure
 Cell Division and Cytogenetics
• Tissue cells of interest
are grown in culture
• Cell must be “frozen” at
metaphase
t h
– 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/zoology/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
 Human Chromosome Basics
C
metacentric

submetacentric
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, proteins, RNA, sugars)
• 3 groups of shapes based on centromere position, arm length
 Example of G-Banding:
Ch
Chromosome 11
• GTL stain:
Giemsa/Trypsin/Leishman
p arm • Chr 11 is submetacentric
• Representative
R t ti ideogram
id
Centromere • Stained to distinguish denser
and less dense areas
• Unique staining 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 Gene?
• DNA sequence
q
begins with a start
codon; ends with a
stop
p codon
• Amino acids (each
with a 3-character
code) then join to
form a protein which
then has a function
• There
Th is
i “filler”
“fill ” DNA
that codes for other
stuff
 So Many Genes
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
p arm 64327 57011q13MIRN125B1 121475.67511MLL
64327.57011q13MIRN125B1 121475 67511MLL 117812.41511q23MRE11A
117812 41511q23MRE11A 93790.11511q21MYEOV
93790 11511q21MYEOV
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
Centromere 6372.93111p15API5 43290.10911APLNR 56757.64311q12APOA1 116211.67911q23-q24ARAP1
72073.76211q13.3ARCN1 117948.32111q23.3ARFIP2 6453.50211p15ARHGAP1
46655.20811p11.2ARHGEF17
46655 20811p11 2ARHGEF17 72697.31711q13.3ARL2
72697 31711q13 3ARL2 64538.16211q13ARRB1
64538 16211q13ARRB1 74654.13011q13ART1
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
q arm 2861 02411p15 5CDON 125331.92311q23
2861.02411p15.5CDON 125331 92311q23-q24CENTD2
q24CENTD2 72073.76211q13.3CEP57
72073 76211q13 3CEP57 95163.29011q21CFL1
95163 29011q21CFL1
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
102485.37011q21-q22.1EED
1531.85711p15.5DYNC2H1 102485.37011q21 85633.46311q14.2-q22.3EHF
q22.1EED 85633.46311q14.2 q22.3EHF 34599.24411p12EI24
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
82211.05611q13-q14GNG3
URL : http://AtlasGeneticsOncology.org/Indexbychrom/idxa_11.html 67107.64211q13-qterGTF2H1 18300.71911p15.1-p14H19 1972.98311p15.5H2AFX 118469.79511q23.3HBB
© Atlas of Genetics and Cytogenetics in Oncology 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
chromosome?
h ?
• Constitutional vs acquired
q abnormalities

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

• Structural abnormalities
– Deletions
– Inversions
– Translocations
Monosomy X: Turner Syndrome
C
Constitutional
i i lLLoss
Trisomy 21: Down Syndrome
C i i lG
Constitutional i
Gain
 Deletion

http://ghr.nlm.nih.gov/handbook/illustrations
 Deletion 5q
A
Acquired
i dL Loss
• Interstitial losses of
the long arm of
chromosome 5
• These
Th llosses result
l iin
large numbers of
genes being lost
• Often associated with
myelodysplastic
syndromes and acute
myeloid leukemia From: http://atlasgeneticsoncology.org/Educ/Images/GeneticCancerFig7.jpg
 Inversions

http://ghr.nlm.nih.gov/handbook/illustrations
 Inversion (3)(q24q27)
A i d Ab
Acquired li
Abnormality

From: http://members.aol.com/chrominfo/images/inv3ideo.gif

• Interstitial
I t titi l segmentt inverts
i t
 Translocations

http://ghr.nlm.nih.gov/handbook/illustrations
 Translocation t(9;22)
A
Acquired
i d Ab
Abnormality
li
• Material is
exchanged between
chromosomes 9 and
22 creating a new
22,
fusion gene: bcr/abl
• 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
Dicentric Chromosome

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

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
– Inversions
I i
– 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 centromeres]
– Duplicate (dup) [duplication of a portion of a chromosome]
– Insertion (ins)
– Isochromosomes (i) [both arms are the same]
– Marker chromosome (mar) [unidentifiable piece of chromosome]
– Ring chromosome (r)
– Hyperdiploidy: greater than 48 chromosomes
 Interpreting Cytogenetic Reporting
• In sequence:
q
– 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 karyotype
• Examples
– 46, XX; t(9;22)(q13;q22) [20]
– 47 XY; +21 [12]
47,
– 46, XX; inv 16(q13; q21) [20]
– 45, XY; -5 [18]; 46, XY [2]
– 46 XY
46, XY; -5
5 (q13) [4]
[4]; 46
46, XX [16]
 Cytogenetic Pioneers
Barbara McClintock
– Fi
Firstt genetic
ti map off maize
i
– Genetic and physical characteristics correlated
– Her work helped explain how cells that share the
same genome can haveh differentt ffunctions
diff ti
– Nobel Prize for transposons in 1983

Janet Rowley
– Hypothesized that leukemias might
contain non-random
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 p
promyelocytic
y y 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)(q11;q34)
( ; )(q ;q )
– Some myelodysplastic patients—
typically older women--had a pattern
of normal platelet counts and a
favorable prognosis
• 5q- syndrome
 Risk Stratification for Acute
L k i U
Leukemias Using
i C Cytogenetics
i
• Previous to Janet Rowley and others’ observations about cytogenetics and prognosis,
leukemias were only categorized by morphology under the microscope

• 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
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
inhib. based chemotherapy (MLL
gene is located at 11q23); usually t(9;11) (p22;q23)
 Pre-TED
Pre TED Form (2)

• IIn the
th pre-TED
TED example l above,
b Ph
Ph+ refers
f tto
the cytogenetics; bcr refers to the detection of
bcr/abl gene product
product, usually by PCR or FISH
Form 2100 Chimerism Studies

• N
Note
t th
thatt for
f collection
ll ti off
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 biology 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
b
become available
il bl
– Anti-bcr/abl drugs: imatinib and 2nd generation drugs
– Anti flt3 etc
etc.
 Summary
• A varietyy 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 (e.g.
g normal cytogenetics
in AML)
• Newer techniques (polymerase chain reaction
[PCR] flfluorescentt in-situ
[PCR], i it h hybridization
b idi ti [FISH])
can assist in searching for occult genetic
aberrations
 Web References

• http://www.slh.wisc.edu/wps/wcm/connect/e
xtranet/cytogenetics/
t t/ t ti /
• http://ghr.nlm.nih.gov/handbook/illustrations