ChromosOmics - Database
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                                                           DIAGNOSTIC TESTING                                                           

Guidelines for and background about UPD testing

Guidelines were developed for UPD testing in Canada. The guidelines were circulated for comment to the CCMG members at large and following appropriate modification, approved by the CCMG Board of Directors (July 2010; updated 2020) {553; 1193}. Prenatal UPD-detection is discussed in {1258}.
Chinese guidelines (
paper partially based on data from this page) see 1348
Also NGS (next generation sequencing) is used now to detect UPD {841}.

In {923} as rare case of point mutation and overlapping exon deletion mutation mimicking a UPD is reported.

Long contigous stretches of homozygosity detected by SNP-array-CGH are discussed to be potentially hints on UPD, too {e.g. 924; 933; 1287}.

In {1051} it is suggested that long stretches of iUPD are in >99% reliable as hint for PWS or AS.

In {1068} it is admitted that SNP-array testing will miss at least 1/3 of UPD cases!! This is highlighted als here {1327}.

Discussion on methods used in paternity testing and how to avoid UPD-mixup is discussed in {1222}.

CRISPR/Cas9 is discussed as tretament option for imprinting disorders including UPD {1231}.

In an exome sequencing setting 16 UPD events were identified in 2675 trios {1340}.

Comparison of different methods for PWS/AS diagnostics {1358}.

When using SNP-array = SNP aCGH

  In SNP-array testing only iUPD is decetable.
Thus iUPD may be mixed up with streches of long contiguous stretches of homozygosity due to
high frequencies of specific genomic regions in a population.

Chromosomal region
Frequency (%)
Reference
1p33p32.3 6 1162
1p32.2p34.1 1.1 1175
1p31.1p31.3 0.8 1175
1q21.2q21.3
21
1162
2p11.2p12 1.3 1175
2q11.1q11.2 9 1162
2q32.1q32.3 1.1 1175
2q32.3q33.1 1.5 1175
3p21.31p21.2 16 828; 933; 1162
4p14p15 0.7 1175
6p21.32p22.2 1.6 1175
6p22.2p22.1 5 933; 1162
7q11.22q11.23 5 1162
8p11.21p11.23 3 1175
8q11.1q12.1 4.2 1175
10q21.1q21.2 3.2 1175
10q22.1q23.31 5 1162
11p13p12 3.6 1175
11p11.2p11.12 19 828; 933; 1162
11q14.1q14.3 0.8 1175
11q21q22.3 0.6 1175
12p12p11.1 1.3 1175
15q15.2q21.1 12 1162
16p11.2p11.1 49 828; 1162
17q22q24.2 1.2 1175
18q11.2q12.1 1.3 1175
18q12.1q12.3 3 1175
20q11.21q11.23 6 1162; 1163


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