Standardised definitions and terminology for human cytogenetic variants
Lynda Campbell
Victorian Cancer Cytogenetics Service
lynda.campbell@svhm.org.au
Cytogenetic nomenclature
• 1956: Tjio and Levan reported that the human
chromosome number was 46 and not 48
• Resulting flurry of publications led to a variety of
nomenclatures and much confusion in the
literature
• The need for a common system of nomenclature
was identified to improve communication
between workers in the field
ISCN
• 1960: a small group convened by Dr Charles
Ford gathered in Denver to formulate a
nomenclature
• The proceedings of the meeting were published
in a report entitled “A Proposed Standard
System of Nomenclature of Human Mitotic
Chromosomes” – this has formed the basis for
all subsequent revisions of the nomenclature
ISCN 2009
Now 16 pages of FISH nomenclature
Separate copy number detection chapter for microarrays and MLPA
Chromosome identification
• Size
• Position of centromere
• G‐banding pattern
• FISH
• Molecular karyotyping
Chromosome identification
• The position of the centromere
provides a useful landmark for dividing chromosomes into karyotype groups and for establishing a standardized nomenclature for mapping the positions of genes on chromosomes • Eukaryotic chromosomes exist in four major types based on the position of the centromere:
• metacentric, • submetacentric, • acrocentric, and • telocentric.
p
p13
centromere
q
q13
q23
Chromosome nomenclature
• Modal number of chromosomes
• Sex chromosome complement
• Any abnormalities of autosomes in numerical order
• Numerical abnormalities precede structural abnormalities for each chromosome
• E.g. 45,XY,‐9,t(9;22)(q34;q11.2)
Numerical abnormalities
• normal chromosome number (46) = diploid
• gain of a chromosome ‐ trisomy = hyperdiploidy
• loss of a chromosome ‐ monosomy = hypodiploidy
45,XY,‐7
Structural abnormalities
• translocation or an exchange between two or more chromosomes
• deletion ‐ loss of part of a chromosome
• inversion ‐ rearrangement within an individual chromosome
Translocations
Gene A
Gene B
A/B fusion gene
B/A fusion gene
Inversion 16
AML M4Eo
Fusion of CBFB on
16q22 and MYH11
gene on 16p13
46,XX,inv(16)(p13q22)
AML with maturation with Auer rods & eosinophilia.
Fuses the RUNX1 gene on 21 with the RUNX1T1 (CBFA2T1, ETO) gene on 8q22
45,X,‐Y,t(8;21)(q22;q22)
Translocations
Gene A
Gene B
Gene A promotor
Results in Gene B upregulation
Carlo Croce’s group showed that MYC was
involved in the t(8;14) of Burkitt Lymphomas and
was up-regulated
46,XX,t(8;14)(q24;q32)
Chromosome variants
Large heterochromatin on chromosome 9: 9qh+
Fragile site on chromosome 10 associated with BrdU: fra(10)(q25)
FISH has made our lives so much easier but the challenge is how to describe what you see!
Fluorescence in situ hybridization
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Painting probes
Translocation probes
Centromere probes
Metaphase and interphase
M‐FISH
Dual fusion FISH probes
1995: nuc ish 9q34(ABLx3),22q11(BCRx3)(ABL con BCRx2)
2005: nuc ish(ABL1x3),(BCRx3)(ABL1 con BCRx2)[400]
2009: nuc ish(ABL1,BCR)x3(ABL1 con BCRx2)[400]
Break‐apart probes
• Metaphase:
– 46,XY,t(11;19)(q23;p13.3).ish
t(11;19)(5’MLL+;3’MLL+)
• Interphase:
– nuc ish(MLLx2)(5’MLL sep 3’MLLx1)
Normal cell
Split signal indicating
translocation
MLL break apart probe
Case study
• 53 year old man presented with pancytopenia and was found to have acute erythroleukaemia
How would we describe this?
Karyotype
• 46,XY,inv(11)(p15q23)[7]/46,XY[13]
• 46,XY,inv(11)(p15q23)[7]/46,XY[13].ish
inv(11)(p15)(3’MLL+)(q23)(5’MLL+,3’MLL+)
• 46,XY,inv(11)(p15q23)[7]/46,XY[13].ish
inv(11)(p15)(3’MLL+)(q23)(5’MLL+,3’MLL+). nuc ish(5’MLLx2,3’MLLx3)(5’MLL con 3’MLLx2)
Probe names
• When available, the clone name is
preferred
• If the clone name is unavailable, use the
locus designation according to GDB or, if
that is unavailable, the gene name
according to HUGO-approved
nomenclature – e.g. ABL1 rather than
ABL; RUNX1 rather than AML1, etc.
Sex‐mismatched transplants
• Female patient receiving SCT from brother:
Donor cells are placed last in the string:
• nuc ish(DXZ1x2)[50]//(DXZ1,DYZ3)x1[350]
• ISCN 2009 clarified the case of full
chimerism:
• //nuc ish(DXZ1x2)[200]
Array nomenclature
• Differentially labelled test and reference DNA applied
to targets arranged on a solid support
• Number and type of clones used as targets (BAC,
cosmid, etc.) is listed in parentheses
• Normal female and male results using whole genome
array:
arr(1-22,X)x2,
arr(1-22)x2,(XY)x1
• Limited arrays – e.g. covering only chromosome 2
– arr(2)x2
• Deletion of 4q identified:
– arr 4q32.2q35.1(163,146,681-183,022,312)x1
Patient with MDS
• 46,XY,del(20)(q11.2)[20].arr 5q31.2(137,736,066x2,137,782,447‐
138,987,704x1,139,017,982x2),20q11.22q11.32(33,785,207x2,
33,852,818‐56,767,187x1,56,698,692x2)
MacKinnon et al, 2011
Array karyotype (Oncoglyphix)
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arr 2p11.2(89,257,482‐89,276,547)x0,
2p11.2(89,315,265‐89,325,297)x0,2p11.2(89,613,887‐89,624,078)x0,
2p11.2(89,663,137‐89,680,741)x0,
3p22.1p21.31(40,634,611‐49,200,205)x1,
3p12.2p12.1(83,454,302‐84,568,449)x1,3q11.2(97,007,703‐98,017,504)x1,
5p15.33q35.3(129,331‐180,619,169)x3,8q12.1q12.3(58,374,940‐62,633,890)x1,
9p23p22.3(12,907,152‐16,228,956)x1,
9p22.3p21.1(16,261,328‐30,034,167)x0,
9p21.1(31,659,680‐31,832,129)x1,
9p13.2(36,984,750‐37,014,347)x>4,
11q22.3(107,132,679‐109,709,712)x1,11q23.2q23.3(114,153,819‐116,706,955)x1,
12q21.33(90,847,497‐91,060,832)x1,
14q32.33(105,265,167‐105,399,507)x1,14q32.33(105,399,628‐105,452,989)x0,
14q32.33(105,452,999‐105,466,192)x1,14q32.33(105,466,932‐105,511,549)x0,
14q32.33(105,516,392‐105,896,815)x1,
22q11.22(20,716,186‐20,930,051)x1,22q11.23(22,674,846‐22,723,991)x0 Abnormal Male Array karyotype (Oncoglyphix)
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arr 2p11.2(88,932,826‐89,912,623)x1,
9p24.3p21.3(188,160‐21,132,703)x1,
9p21.3(21,132,763‐23,416,830)x0,
9p21.3p13.2(23,416,890‐36,778,992)x1,
14q32.33(105,401,418‐105,597,823)x0,
14q32.33(105,642,023‐106,340,244)x1,
20q11.21q13.33(30,646,941‐62,359,694)x1,
22q11.22(20,643,480‐20,908,795)x1 Abnormal Male Conclusion
• Inevitably, with a field that is changing rapidly,
there will be areas not covered or inadequately
addressed. However, there has been significant
progress since the initial attempts at FISH
nomenclature in ISCN 1995 and array
nomenclature in 2005.