ChromosOmics - Database

Icon by Leon Liehr                   

                                            - Patient and user information -                                           

How to use this pape

 The start page is self explaining.
Problems might appear with the chromosome-specific pages, which are explained below.
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The chromosome-specific pages are in general organized in the following way:
For each chromosome one sub-page has been created, which can be accessed by the following general table.
All cases written in black in this example table lead sSMC cases of one specific type.
Cases may have no clinical impact (green), clinical impact (red) or the clinical correlation is not known (gray).
Also the sSMC may not be have a normal centromere, but a so-called neocentromere (yellow); such cases may be found in clinical patients or in tumors.
Cases were the clinical correlation is not known due to presence of a complex sSMC,
a discontinous sSMC or a uniparental disomie (UPD) are listed as seperate ‚gray‘ subgroups.
Finally, clinical cases with similar imbalances as induced by an sSMC, but due to duplication, insertion or another rearrangement are also linked by the three fields
(green, red, gray or yellow) highlighted here in gray letters. „n“ stands for the number of corresponding cases included in this collection.
In some subpages additional subgroups of chromosome-specific sSMC were included in the table below.

Cases without clinical findings
n
Similar imbalances –
no sSMC

n
Cases with clinical findings
n
Similar imbalances –
no sSMC

n
Cases without clear clinical correlation
n
Cases with discontinous sSMC
n
Cases with complex sSMC

n
Cases with UPD and sSMC
n
Cases with neocentromeres
n
Similar imbalances -
no sSMC

n
tumor
n
DISCLAIMER
References

The diclaimer and the reference link lead to the corresponding pages.
Below the colored table leads to the UPD-database.

UPD (uniparental disomy) cases:
UPD(n)mat
UPD(n)pat
UPD(n)mat or pat

This whole part is interactive - by clicking one reaches the corresponding single cases.


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  The probably non-dosage sensitive pericentric region of each chromosome is given for all pages, where it is appropriate as
- schematic cytogenetic depiction
- schematic molecular-cytogenetic depiction

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References

References of each sub-page may be provided separately.

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Cases are characterized according to the following parameters
case no.
gender/
age at diagnosis

studied
material

de novo/
inherited

GTG-banding result
grade of mosaicism

final result of the sSMC
test
methods

clinical symptoms
eference

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 The case numbers (case no.) are constructed as follows:
If all information is available for a case, it is numbered according to the sSMCs breakpoint in the short arm
of the corresponding chromosome starting from pter (= end of the short arm - see example 1). 
Exception: as all acrocentric chromosomes start always with the whole short arm for chrs. 13-15 and 21-22
the breakpoints in the long arm (q-arm) are relevant for case numbers;
here the starting point is the centromere (q10 - see example 2). 
In cases with neocentromeres the same system is applied - starting from p-arm. (see example 3).

example 1
chromosome -
information if sSMC-carrier was clinically normal (= O) or with clinical signs (= W) -
breakpoint (as described above)/
variant number - case number with this variant

01-
O-
p12/
1-1

Described is a clinically healthy carrier of an sSMC(1), with the breakpoint in 1p12; it is a variant called '1' (here: carrier of a centric minute shaped sSMC) and case 1 described
example 2
chromosome -
information if sSMC-carrier was clinically normal (= O) or with clinical signs (= W) -
breakpoint (as described above)/
variant number - case number with this variant

15-
O-
q11/
2-2

Described is a clinically healthy carrier of an sSMC(15) with the breakpoint in 15q11; it is a variant called '2' (carrier of[nbsp] two inverted duplicated shaped sSMC), as another variant was already described with the same breakpoint, and case 2 described for this condition
example 3
chromosome -
information if sSMC-carrier was clinically normal (= O) or with clinical signs (= W) -
breakpoint (as described above)/
variant number - case number with this variant

14-
N-
qt32.1/
1-1

Described is a clinically abnormal carrier of a neocentric sSMC(14) with the breakpoint in 14q32.1; it is a variant called '1', and case 1 described for this condition.

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If not all relevant information for an sSMC carrier are available this enumeration system can not be applied:     
when the sSMC is not characterized in detail, but the clinical outcome is known,
the cases described in the literature are numbered consecutively (acc. to their inclusion in this data base)
as 'CO'-cases (no clinical symptoms present in sSMC carrier) or 'CW-cases' (clinical symptoms present in sSMC-carrier)
.


example 4
chromosome -
special abbreviation -
variant number

01-
CW-
5

Described is a carrier of a not in detailed characterized sSMC(1) = 01; he is not healthy = CW; it is the 5th case included in this page = 5

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When the sSMC is characterized in detail or not, and the clinical outcome is not known,
 the case is summarized under the 'U-cases' = cases with unclear clinical correlation of the sSMC.
In this group also cases are summarized where apart from one specific sSMC a second sSMC
or another chromosomal aberration is present;
 here also the influence of the sSMC on the clinical phenotype cannot be determined.



example 5
chromosome -
special abbreviation -
variant number

02-
U-
1

Described is a carrier of a not in detailed characterized sSMC(2) = 02; the pregnancy was terminated and no clinical information on the carrier with the sSMC is available = U; it is the 1st such case included in this page = 1
example 6
chromosome -
special abbreviation -
variant number

03-
U-
1

is a carrier of a not in detailed characterized sSMC(3) = 03; moreover a second not characterized sSMC is present; thus, it is not clear where the described clinical symptoms come from = U; it is the 1st such case included in this page = 1

Finally, in case of some special conditions additional abbreviations were introduced on the corresponding sub-pages
e.g. for derivative chromosome 22 syndrome = der(22): 22-Wder-189 = derivative sSMC derived from chromosome 22;
with clinical symptoms and a der(22)-typical sSMC (Wder); case 189 included in this page  


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Abbreviations and FISH-methods used are specified here:
Karyotype formulas are not always provided according to the
international standard system for cytogenetic nomenclature (ISCN) {11}



Abbreviations
FISH-and other Methods
AF
amniocytic fluid cells
acro-cenM
acrocentric chromosome specific multicolor-FISH {1}
CH
chorion biopsy cells
aCGH
array based comparative genomic hybridization {2}
DD
DYS
developmental delay
dysmorphism
acro M
M-FISH for acrocentric chromosomes {3}
m
MR
months
mental retardation
cenM centromere specific multicolor FISH {4}
n.a.
not available
cep
centromeric probes
PBL
peripheral blood
CGH
comparative genomic hybridization {5}
PL
placenta
MCB
multicolor banding {6}
TOP
termination of pregnancy
M-FISH
multiplex-FISH using whole chromosome painting probes {7}
w
weeks
midi
NGS
microdissection {8}
Next Generation Sequencing
y
years
subcenM
subcentromere-specific multicolor-FISH {9}
*
karyotype interpretation
according to results in paper

SKY
spectral karyotyping using whole chromosome painting probes {10}


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Method-References:
  1. Trifonov V, Seidel J, Starke H, Martina P, Beensen V, Ziegler M, Hartmann I, Heller A, Nietzel A, Claussen U, Liehr T.
    Enlarged chromosome 13 p-arm hiding a cryptic partial trisomy 6p22.2-pter.
    Prenat Diagn. 2003 May;23(5):427-430.[nbsp]

  2. Vermeesch JR, Melotte C, Salden I, Riegel M, Trifnov V, Polityko A, Rumyantseva N, Naumchik I, Starke H, Matthijs G, Schinzel A, Fryns JP, Liehr T.
    Tetrasomy 12pter-12p13.31 in a girl with partial Pallister-Killian syndrome phenotype.
    Eur J Med Genet. 2005 Jul-Sep;48(3):319-327.

  3. Langer S, Fauth C, Rocchi M, Murken J, Speicher MR.
    AcroM fluorescent in situ hybridization analyses of marker chromosomes.
    Hum Genet. 2001 Aug;109(2):152-158.

  4. Nietzel A, Rocchi M, Starke H, Heller A, Fiedler W, Wlodarska I, Loncarevic IF, Beensen V, Claussen U, Liehr T.
    A new multicolor-FISH approach for the characterization of marker chromosomes: centromere-specific multicolor-FISH (cenM-FISH).
    Hum Genet. 2001 Mar;108(3):199-204.[nbsp]

  5. Liehr T, Heller A, Starke H, Rubtsov N, Trifonov V, Mrasek K, Weise A, Kuechler A, Claussen U.
    Microdissection based high resolution multicolor banding for all 24 human chromosomes.
    Int J Mol Med. 2002 Apr;9(4):335-339.

  6. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D.
    Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors.
    Science. 1992 Oct 30;258(5083):818-821.

  7. Speicher MR, Gwyn Ballard S, Ward DC.
    Karyotyping human chromosomes by combinatorial multi-fluor FISH.
    Nat Genet. 1996 Apr;12(4):368-375.

  8. Senger G, Chudoba I, Friedrich U, Tommerup N, Claussen U, Brøndum-Nielsen K.
    Prenatal diagnosis of a half-cryptic translocation using chromosome microdissection.
    Prenat Diagn. 1997 Apr;17(4):369-374.

  9. Starke H, Nietzel A, Weise A, Heller A, Mrasek K, Belitz B, Kelbova C, Volleth M, Albrecht B, Mitulla B, Trappe R, Bartels I, Adolph S, Dufke A, Singer S, Stumm M, Wegner RD, Seidel J, Schmidt A, Kuechler A, Schreyer I, Claussen U, von Eggeling F, Liehr T.
    Small supernumerary marker chromosomes (SMCs): genotype-phenotype correlation and classification.
    Hum Genet. 2003 Dec;114(1):51-67.

  10. Schröck E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, Garini Y, Ried T.
    Multicolor spectral karyotyping of human chromosomes.
    Science. 1996 Jul 26;273(5274):494-497.

  11. ISCN : An International System for Human Cytogenetic Nomenclature
  12. NGS-explanation



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