Molecular cytogenetics (FISH)

Molecular cytogenetics (fluorescence in-situ hybridisation, FISH) combines classic cytogenetic methods with molecular genetic techniques.

FISH allows detecting nucleic acids directly in tissues, cell nuclei or chromosomes. Specific oligonucleotides marked with fluorescent dye are used as probes to detect chromosome microsections that can be visualised under a fluorescence microscope.

The method of fluorescence in-situ hybridisation can be performed on metaphase chromosomes and on interphase nuclei.

Indications

  • metaphase FISH: to excluded microdeletions and other chromosomal aberrations
  • interphase FISH / prenatal rapid test: for quick detection of the most common trisomies 13, 18 and 21 and the sex chromosomes
  • characterisation of malignant tumours

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Sampling / shipping

Metaphase FISH: to exclude microdeletions and other chromosome aberrations

  • Lithium heparin blood
    Newborns: 1 – 2.5 ml
    Children and adults: 5 – 7 ml
    Duration*: 5 – 7 days
  • on cultivated amniotic fluid or CVS material
    Amniotic cells  approx. 10 – 15 ml amniotic fluid
    Discard the first 2 ml. Store and transport at room temperature. Never centrifuge!
    Register sample by phone  (+49 6132 781 411) / fax  (+49 6132 781 194) with the Client Service of Human Genetics
    Duration*: 8 – 10 days
    Chorionic villi (CVS) 
    min. 20 – 30 mg chorionic villi,
    Use sterile transport medium (available upon request)
    Register sample with the Client Service (see above) by telephone or fax
    Duration*: direct preparation 1 – 2 days; culture 8 – 10 days
    Duration*: 10 – 14 days
  • List of available probes available upon request
  • Interphase FISH / prenatal rapid test. Additionally 3 ml of amniotic fluid required. Not possible on bloody amniotic fluid samples.
    Only performed in combination with the conventional chromosome analysis.
    Duration*: 24 – 48 hours
  • Tumour FISH using bone marrow sample
    (minimum 10 x 106 mononuclear cells) 5 – 10 ml heparinised bone marrow aspirate+
    Duration*: 5 – 10 days
    or
  • Leukemia blood(blast count ≥ 20 %) 5 – 10 ml heparinised peripheral blood+
    Duration*: 5 – 10 days
    MACS (magnetic enrichment of CD138 positive plasma cells) additionally 3 ml bone marrow / peripheral blood
    + heparin concentration 10 – 25 IU / ml blood

Request forms:

Prenatal: Prenatal diagnostics

Postnatal: Postnatal diagnostics chromosome analysis
Duration* = Processing time after arrival of the sample in the laboratory

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Hematologic probes

ALK t(2p23)

ATM (11q22.3) and TP53 (17p13.1)

B-CLL probe panel (CEP12 [D12Z1], D13S319 [13q14.3], LSI13q34, ATM [11q22.3], TP53 [17p13.1])

BCL6 t(3q27)

BCR/ABL1 t(9;22)(q34;q11.2)

CBFB/MYH11 inv(16)(p13q22)/t(16q22)

CCND1/IGH t(11;14)(q13;q32)

CCND3/IGH t(6;14)(p21;q32)

CDKN2A (p16, 9p21) ) together with checking D9Z1

CDKN2C (p18,1p32.3) and CKS1B (1q21)

Centromere 3 (D3Z1)

Centromere 4 (D4Z1)

Centromere 6 (D6Z1)

Centromere 7 (D7Z1)

Centromere 8 (D8Z2)

Centromere 9 (D9Z1)

Centromere 10 (D10Z1)

Centromere 11 (D11Z1)

Centromere 12 (D12Z1)

Centromere 12 (D12Z1), D13S319 (13q14.3) and LSI13q34

Centromere 15 (D15Z4)

Centromere 16 (D16Z3)

Centromere 17 (D17Z1)

Centromere 18 (D18Z1)

Centromere X/Y (DXZ1/DYZ3)

D7S486 (7q31) together with checking in 7q11.23

D20S108 (20q12)

D13S319 (13q14.3), LSI13q34 and centromere 12 (D12Z1)

EGR1 (5q31) together with checking in 5p15.2

ETV6/RUNX1 t(12;21)(p13;q22)

E2A (TCF3) t(19p13.3)

FGFR3/IGH t(4;14)(p16;q32)

IGH t(14q32)

IGH/BCL2 t(14;18)(q32;q21)

IGH/CCND1 t(11;14)(q13;q32)

IGH/CCND3 t(6;14)(p21;q32)

IGH/FGFR3 t(4;14)(p16;q32)

IGH/MAFA t(14;16)(q32;q23)

IGH/MAFB t(14;20)(q23;q12)

KMT2A(MLL) t(11q23)

KMT2A(MLL)/AFF1(AF4) t(4;11)(q21.3-q22.1;q23.3)

KMT2A(MLL)/MLLT1(ENL) t(11;19)(q23.3;p13.3)

KMT2A(MLL)/MLLT3(AF9) t(9;11)(p21.3;q23.3)

KMT2A(MLL)/MLLT4(AF6) t(6;11)(q27;q23.3)

MALT1 t(18q21)

MYB (6q23) and D6Z1

MYC t(8q24)

MYC/IGH t(8;14)(q24;q32) + D8Z1

PDGFRA/CHIC2/FIP1L1 (4q12)

PDGFRB (5q32)

PML/RARA t(15;17)(q24.1;q21.1)

RB1 (13q34) together with checking in 21q22.13

RPN1/MECOM t(3;3)(q21.3;q26.2)/ inv(3)(q26.2)

RUNX1T1/RUNX1 t(8;21)(q22;q22)

TCF3/PBX1 t(1;19)q23;p13.3)

TCRa/d t(14q11)

TET2 (4q24) together with checking in 4q12

TP53 (17p13.1) and ATM (11q22.3)

ZNF44/ZNF443/MAN2BA:19p13;GLTSCR1/GLTSCR2/CRX:19q13

Other hematologic probes available upon request

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Probes microdeletion syndromes

 

Angelman

Cri-du-Chat

DiGeorge-/Velocardiofacial-1

DiGeorge-/Velocardiofacial-2

Miller-Dieker

Prader-Willi

Smith-Magenis

Williams-Beuren

Wolf-Hirschhorn

1p Microdeletion

Localisation

15q11.2

5p15.2

22q11.2

10p14

17p13.3

15q11.2

17p11.2

7q11.23

4p16.3

1p36

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Prenatal "FISH rapid test" for aneuploidy screening

Specific probes for the chromosomes X, Y, 13, 18 and 21

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Chromosome-specific probes

Chromosome 1 Localisation
tel 1p  (not published at present) 1p36.3
tel 1q  (D1S3738) 1q44
LSI p58/LSI telomere 1p/LSI 1q25 1p36/1q25
Staining of whole chromosome 1 (WCP1)
Chromosome 2 Localisation
tel 2p (VIJ2yRM2052) 2p25
tel 2q (D2S447) 2q37
Staining of whole chromosome 2 (WCP2)
Chromosome 3 Localisation
tel 3p (D3S4559) 3p26
tel 3q (D3S4560) 3q29
D3Z1 Centromere
Staining of whole chromosome 3 (WCP3)
Chromosome 4 Localisation
tel 4p (D4S3359) 4p16.3
tel 4q (D4S2930) 4q34
LSIWHSC1,Wolf-Hirschhorn syndrome 4p16.3
D4Z1 Centromere
Staining of whole chromosome 4 (WCP4)
Chromosome 5 Localisation
tel 5p (STS84c11) 5p15.3
tel 5q (not published at present) 5q35.3
D5S23, cri du chat syndrome 5p15.2
EGR1 5q31
CSF1R 5q33.3-q34
Staining of whole chromosome 5 (WCP5)
Chromosome 6 Localisation
tel 6p (not published at present) 6p25
tel 6q (VIJ2yRM2158) 6q27
D6Z1 Centromere
Staining of whole chromosome 6 (WCP6)
Chromosome 7 Localisation
tel 7p (VIJ2yRM2158) 7p22
tel 7q (STS2000H) 7q36
ELN/LIMK1/D7S613,Williams-Beuren syndrome 7q11.23
D7S486/D75522 7q31
D7Z1 Centromere
Staining of whole chromosome 7 (WCP7)
Chromosome 8 Localisation
tel 8p (D8S504) 8p23
tel 8q (VIJ2yRM2053) 8q24.3
D8Z2 Centromere
Staining of whole chromosome 8 (WCP8)
Chromosome 9 Localisation
tel 9p (not published at present) 9p24
tel 9q (D9S325) 9q34.3
D9Z1 Centromere
Staining of whole chromosome 9 (WCP9)
Chromosome 10 Localisation
tel 10p (10p006) 10p15
tel 10q (D10S2490) 10q26.3
DGCR2,DiGeorge/VCF syndrome 2 10p14
D10Z1 Centromere
Staining of whole chromosome 10 (WCP10)
Chromosome 11 Localisation
tel 11p (D11S2071) 11p15.5
tel 11q (VIJ22072) 11q25
D11Z1 Centromere
Staining of whole chromosome 11 (WCP11)
Chromosome 12 Localisation
tel 12p (STSsAVH27) 12p13.3
tel 12q (VIJ2YRM2196) 12q24.33
D12Z1 Centromere
Staining of whole chromosome 12 (WCP12)
Chromosome 13 Localisation
tel 13q (D13S327) 13q34
LSI 13 (D13S917/RB1) 13q14.4
D13Z1/D21Z1 Centromere
Staining of whole chromosome 13 (WCP13)
Chromosome 14 Localisation
tel 14q (D14S308) 14q32
D14Z1/D22Z1 Centromere
Staining of whole chromosome 14 (WCP14)
Chromosome 15 Localisation
tel 15q (D15S396) 15q26
D15Z4 Centromere
D15Z1 15p11.
D15S11 15q11-15q13
SNRPN, Prader-Willi/Angelman syndrome 15q11-15q13
UBE3A/D15S10, Prader-Willi/Angelman syndrome 15q11-15q13
Staining of whole chromosome 15 (WCP15)
Chromosome 16 Localisation
tel 16p (D16S3400) 16p13.3
tel 16q (16q013) 16q24
D16Z2 Centromere
Staining of whole chromosome 16 (WCP16)
Chromosome 17 Localisation
tel 17p (D17S2199) 17p13
tel 17q (D17S928) 17q25
LIS1, Miller-Dieker syndrome 17p13.3
FLII/TOP3/SHMT1, Smith-Magenis syndrome 17p11.2
Miller-Dieker (LIS1)/Smith-Magenis syndrome (RAI) 17p13.3/17p11.2
RARA 17q21.1
D17Z1 Centromere
Staining of whole chromosome 17 (WCP17)
Chromosome 18 Localisation
tel 18p (D18S552) 18p11.3
tel 18q (VIJ22050) 18p23
D18Z1 Centromere
Staining of whole chromosome 18 (WCP18)
Chromosome 19 Localisation
tel 19p (not published at present) 19p13.3
tel 19q (D19S238E) 19q13.4
LSI 19p13/LSI 19q13 19p13/19q13
Staining of whole chromosome 19 (WCP19)
Chromosome 20 Localisation
tel 20p (D20S1157) 20p13
tel 20q (not published at present) 20q13.3
LSI 20, D20S108 20q12
Staining of whole chromosome 20 (WCP20)
Chromosome 21 Localisation
tel 21q (D21S1219/D21S1220) 21q22.3
D21Z1/D13Z1 Centromere
LSI 21 (D21S1972/D21S1440/D21S1238/D21S1883) 21q22.13
Staining of whole chromosome 21 (WCP21)
Chromosome 22 Localisation
tel 22q (STS MS607) 22q13.3
D22Z1/D14Z1 Centromere
D22S553/S609/S942, DiGeorge /VCF syndrome 1 22q11.2
ARSA 22q13.3
Staining of whole chromosome 22 (WCP22)
Chromosome X Localisation
tel Xp/Yp (DXYS129/DXYS153) Xp22.3/Yp11.3
tel Xq/Yq (SYBL1) Xp28 /Yq12
DXZ1 in combination with SRY Centromere X + Yp11.3
DXZ1 Centromere X
Staining of whole chromosome X (WCPX)
Chromosome Y Localisation
tel Xp/Yp (DXYS129/DXYS153) Xp22.3/Yp11.3
tel Xq/Yq (SYBL1) Xp28 /Yq12
DXZ1 in combination with SRY Yp11.3 + centromere X
DYZ3 Centromere Y
DYZ1 Heterochromatin region
Staining of whole chromosome Y (WCPY)
Prices of FISH probes on request

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