PWG Quality and Training 2019

ISCN 2020 Ros Hastings

Consultant GenQA,

ISCN Standing Committee

Oxford University Hospitals

NHS Foundation Trust NHS Lothian, Edinburgh

Collaboration between CEQAS and UK NEQAS for Molecular Genetics

Member of consortium

PWG Quality Issues and Training 2019

ISCN - Common misconceptions

and frequent errors

Ros Hastings GenQA

Common Misconceptions

No need to read the whole book

Only look at section with type of abnormality

No logic in the ISCN nomenclature

It is helpful to describe polymorphism in ISCN

pter and qter can be used to describe terminal bands

Normal FISH results cannot be reported in one string

Can if same number of interphase cells analysed from

different hybridisations. Cannot for abnormals.

There are basic rules in ISCN

Basic ISCN Rules

There are basic rules in ISCN

Describe abnormality from pter to qter (no

exceptions in ISCN 2020)

Cell numbers only given for mosaics and clones

Chromosome number order – lowest to highest

Numerical followed by structural aberrations in

chromosomal order

Structural aberrations listed alphabetically

FISH the numerator is the number of abnormal cells, the

denominator is the total of number of cells (12/50).

FISH – only abnormal cells lines same probe, list each

Contigs must either be given in full in ISCN or text

Normal controls not given in ISCN (text only)

Basic ISCN Rules - 2

Can combine short and detailed form of ISCN

When multiple techniques and mosaic – G-banding

first; then FISH, then array, then seq (each separated

by a full stop)

Can list on separate lines but must have a ‘.’ after

each line

For arrays [0.6] and 2~3 are required – either option

in ISCN

rsa ISCN is platform agnostic

rsa- If nucleotides positions are available they should

be included. If not the kit name is given.

Common Errors - 1

Mixing interphase and metaphase FISH

Normals x2 for both

Structurally normal for metaphase FISH x2

Structurally abnormal metaphase FISH - only describe

the derivative chromosome

++/+/- etc for signal pattern

Abnormal interphase FISH - x3 or x1 etc

For breakapart and fusion probes describe the signal

pattern first

Common Errors - 2

Inappropriate use of ‘rec’

Not using ‘der’ when required

A recombinant is a structurally rearranged

chromosome with a new segmental composition

resulting from meiotic crossing over

Derivative chromosomes are products of the original

rearrangement and segregate without further changes

‘add’ can be used when the additional material is of

unknown origin but this can be misleading as there may

be loss of material. ‘der’ is a better term

Common Errors - 3

When do you change the breakpoints?

When FISH or array extend the breakpoints from G-

banding

Optional whether or not repeat breakpoints in the FISH

ISCN if the same as the G-banded ISCN

46,XY,t(4;11)(q21;q23)[6]/47,XY,+der(4)t(4;11),t(4;11)[8].ish

der(4)(MLL+;MLL-)

or

46,XY,t(4;11)(q21;q23)[6]/47,XY,+der(4)t(4;11),t(4;11)[8].ish

der(4)t(4;11)(q21;q23)(MLL+;MLL-)

Common Errors - 4

Random losses vs composite karyotype

42,XX,-2,-16,-21,-22 random losses not clonal don’t include

44,XX,-1,-7,+8,-11

44,XX,-7,+8,-12,-13

43,XX,-7,-18,-20

46,XX,-7,+8

43~46,XX,-7,+8[cp4]

Clone definition: Loss - 3 cells ; Gain- 2 cells

Common Errors - 5

Sequencing has two lines

Use both when know the type of rearrangement

Use HGVS only when cannot deduce rearrangement

e.g. ins or inv or marker

seq[GrCh37] dup(8)(q24.21q24.21)

chr8:128746677_128749160dup

Collaboration between CEQAS and UK NEQAS for Molecular Genetics

Member of consortium

PWG Quality Issues and Training 2019

ISCN 2020

ISCN committee

Standing committee Chair- Jean McGowan- Jordan (CAN)

Cynthia Morton (USA)

Laura Conlin (USA)

Ros Hastings (UK)

Nils Mandahl (SE)

Sarah Moore (AUS)

Jin-Yeong Han (SKR)

Johann Dunnen (NL) - HGVS

Karger Press

2020 version – major revision

Book and online

ISCN 2020 - Karger

Major review

222 suggestions – 4 days

Sequence chapter- more examples

rsa chapter - more examples

Section 13.6 CGH chapter to be removed

Section 8.4 UPD put under array

Polar Body ISCN

Correction of few errors in ISCN 2016

Further clarification of text where needed

Consistency

Online version proposed plus a training module - Karger

Karyotyping FISH Array rsa seq

XX/XY first first last last

last

pter to qter ± + + + +

Cell numbers ± ± - - -

Mosaicism + + 2~3 or

ratio

2~3 -

Genome build - - + + +

ISCN 2016 - inconsistencies

ISCN 2020 – proposed changes

Basic rules at front of book

Sex chromosomes will be reported first for all techniques

Describe abnormality from pter to qter for all techniques so

consistent with ‘arr’ and ‘seq’ nomenclature

Nucleotides can be separated by commas but not full stops

When an unbalanced derivative is inherited from a

balanced rearrangement in the parent ‘dmat’ and ‘dpat’ will

be used as mat or pat implies the parent is unbalanced

Abnormal example of ‘endo’ will be given

Specify which HGVS version being used for ‘seq’

nomenclature

More p-arm examples

Report what you see

Collaboration between CEQAS and UK NEQAS for Molecular Genetics

Member of consortium

PWG Quality Issues and Training 2019

ISCN – Case scenarios

Ros Hastings GenQA

Which is correct?

46,XX,+21,i(21)(q10)

or

46,XX,+21,der(21;21)(q10;q10)

Case 1

Which is correct?

46,XX,+21,i(21)(q10) – for isochromosomes you do not have

+21. Different mechanism for a ‘der’.

or

46,XX,+21,der(21;21)(q10;q10) Should use der unless proven it is an iso

Case 1

Which is correct?

46,XY,add(5)(q31).ish

der(5)del(5)(q11.2q31)ins(5;?)(q32;??)(FISH loci)

or

46,XY,add(5)(q31).ish

der(5)del(5)(q11.2q31)ins(5;?)(q32;?)(FISH loci)

Case 2

Which is correct?

46,XY,add(5)(q31).ish

der(5)del(5)(q11.2q31)ins(5;?)(q32;??)(FISH loci)

or

46,XY,add(5)(q31).ish

der(5)del(5)(q11.2q31)ins(5;?)(q32;?)(FISH loci)

Case 2

Translocation between 5q and 9p where the translocated 5 also had deletion

of the q arm from the breakpoint of the translocation.

Which is correct?

46,XX,der(5)del(5)(q21q34)t(5;9)(q35;p13),der(9)t(5;9) or

46,XX,t(5;9)(q35;p13)del(5)(q21q34)

Case 3

Translocation between 5q and 9p where the translocated 5 also had deletion

of the q arm from the breakpoint of the translocation.

Which is correct?

46,XX,der(5)del(5)(q21q34)t(5;9)(q35;p13),der(9)t(5;9) or

46,XX,t(5;9)(q35;p13)del(5)(q21q34)

Case 3

Triple colour probe MECOM rearrangements showing 1RGA 1RG 1GA due to t(2;3). MECOM is split.

Which is correct?

nuc ish(GOLIM4x2,MECOMx3,MYNNx2)(GOLIM4 con

MECOM sep MECOM con MYNNx1)[100]

nuc ish(GOLIM4,MECOM,MYNN)x2(5’MECOM sep

3’MECOMx1)[100] or

Case 4

Triple colour probe MECOM rearrangements showing 1RGA 1RG 1GA due to t(2;3)

Which is correct?

nuc ish(GOLIM4x2,MECOMx3,MYNNx2)(GOLIM4 con

MECOM sep MECOM con MYNNx1)[100]

nuc ish(GOLIM4,MECOM,MYNN)x2(5’MECOM sep

3’MECOMx1)[100] or

Case 4

Which is correct?

47,XY,+dic(15;15)(q11.1;q11.1).ish

dic(15;15)(D15Z1++,D15Z4++,SNRPN-)

or

47,XY,+dic(15;15)(q11.1;q11.1).ish

dic(15;15)(D15Z1+,D15Z4+,SNRPN-;SNRPN-,D15Z4+,D15Z1+)

Case 5

Which is correct?

47,XY,+dic(15;15)(q11.1;q11.1).ish

dic(15;15)(D15Z1++,D15Z4++,SNRPN-)

or

47,XY,+dic(15;15)(q11.1;q11.1).ish

dic(15;15)(D15Z1+,D15Z4+,SNRPN-;SNRPN-,D15Z4+,D15Z1+)

Case 5

Which is correct?

47,XY,+der(4)t(4;11)(q21;q23),t(4;11)[8]/46,XY,t(4;11)[6]

or

46,XY,t(4;11)(q21;q23)[6]/47,XY,+der(4)t(4;11),t(4;11)[8]

Case 6

Which is correct?

47,XY,+der(4)t(4;11)(q21;q23),t(4;11)[8]/46,XY,t(4;11)[6]

or

46,XY,t(4;11)(q21;q23)[6]/47,XY,+der(4)t(4;11),t(4;11)[8] Stem line goes first not largest clone

Case 6

Which is correct?

47,XY,+der(4)t(4;11)(q21;q23),t(4;11)[8]/48,sl,+19[2]

or

47,XY,+t(4;11)(q21;q23),der(4)(4;11)[8]/48,sl,+19[2]

Case 6a

Which is correct?

47,XY,+der(4)t(4;11)(q21;q23),t(4;11)[8]/48,sl,+19[2] der goes before t if no t(4;11) stem cell clone

or

47,XY,+t(4;11)(q21;q23),der(4)(4;11)[8]/48,sl,+19[2]

Case 6a

Which is correct?

rsa(13)x2,(18)x3,(21)x2

or

rsa(18)x3,(13,21)x2

Case 7

Which is correct?

rsa(13)x2,(18)x3,(21)x2

ISCN 2020: rsa(X,13)x2,(18)x3,(21)x2 or

rsa(X,Y)x1,(13)x2,(18)x3,(21)x2

or

rsa(18)x3,(13,21)x2

Case 7

Which is correct?

45,X[5]/46,X,i(Y)(p10)[5]/46,XY[5].ish i(Y)(SRY-)

or

45,X[5]/46,X,i(Y)(p10)[5].ish i(Y)(SRY-)/46,XY[5]

Case 8

Which is correct?

45,X[5]/46,X,i(Y)(p10)[5]/46,XY[5].ish i(Y)(SRY-)

or

45,X[5]/46,X,i(Y)(p10)[5].ish i(Y)(SRY-)/46,XY[5]

Case 8

Collaboration between CEQAS and UK NEQAS for Molecular Genetics

Member of consortium

PWG Quality Issues and Training 2019

Q & A

Ros Hastings GenQA