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DIAGNOSTIC 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; 1550}
Also NGS (next generation sequencing) is used now to detect UPD {841; 1670}.
A technical standard of the American College of Medical Genetics and Genomics (ACMG) for UPD diagnsotics was issued in 2021 / 2022 {1381}.
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}.
Suggestion how to handle diagnostics of Silver-Russel syndrome {1431}.
Diagnosis of Prader-Willi syndrome and Angelman syndrome by targeted nanopore long-read sequencing can be done {1462}.
altAFplotter: a web app for reliable UPD detection in NGS diagnostics published in {1560}. direct link here
UPD test is done in PID semiroutinely also {1639; 1650} and in induced pluripotent stem cells {1707}.
A kind of guide how to deal with UPD in NIPT is published in 2025 {1708}.
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.
See also {1641 and 1718-1720}
| Chromosomal region |
Frequency (%) |
Reference |
| 1p36.11p35.2 | 1.1 | 1723 |
| 1p33p32.3 | 6-12 | 1162; 1723 |
| 1p32.2p34.1 | 1.1 | 1175 |
| 1p31.1p31.3 | 0.8 | 1175 |
| 1q21.2q21.3 |
17.7-21 |
1162;
1723 |
| 2p11.2p12 | 1.3 | 1175 |
| 2q11.1q11.2 | 4-9 | 1162;
1723 |
| 2q32.1q32.3 | 1.1-1.5 | 1175;
1723 |
| 2q32.3q33.1 | 1.5 | 1175 |
| 3p21.31p21.2 | 2.12-20.3 | 828; 933; 1162; 1723; 1733 |
| 3p12.3p12.1 | 1.2 | 1723 |
| 3q26.1q26.2 | 1.0 | 1723 |
| 4p14p15 | 0.7 | 1175 |
| 5p13.1p12 | 1.2 | 1723 |
| 5q31.2q31.3 | 1.0 | 1723 |
| 6p21.32p22.2 | 1.6 | 1175 |
| 6p22.2p22.1 | 1.5-5 | 933;
1162; 1723 |
| 7q11.22q11.23 | 3.5-5 | 1162;
1723 |
| 8p11.21p11.23 | 3 | 1175;
1723 |
| 8q11.1q12.1 | 4.2 | 1175 |
| 8q23.1q23.3 | 1.2 | 1723 |
| 10q21.1q21.2 | 3.2 | 1175 |
| 10q22.1q23.31 | 1.5-5 | 1162;
1723 |
| 11p13p12 | 3.6 | 1175 |
| 11p12 | 18.2 | 1723 |
| 11p11.2p11.12 | 4.45-19 | 828;
933; 1162; 1733 |
| 11q14.1q14.3 | 0.8 | 1175 |
| 11q21q22.3 | 0.6 | 1175 |
| 12p12p11.1 | 1.3 | 1175 |
| 12q21.1q21.33 | 1.1 | 1723 |
| 12q24.11q24.31 | 2.0 | 1723 |
| 15q15.2q21.1 | 2.8-12 | 1162;
1723 |
| 15q22.2q22.32 | 1.4 | 1723 |
| 16p11.2p11.1 | 2.12 | 1733 |
| 16q11.1q11.2 | 49 | 828; 1162 |
| 16q11.2q12.1 | 1.2 | 1723 |
| 16q21q22.2 | 1.0 | 1723 |
| 16q22.1q22.3 | 1.2 | 1723 |
| 17p11.2p11.1 | 1.6 | 1723 |
| 17q21.2q21.32 | 1.6 | 1723 |
| 17q22q24.2 | 1.2-2.8 | 1175;
1723 |
| 18q11.2q12.1 | 1.3 | 1175 |
| 18q12.1q12.3 | 3 | 1175 |
| 20q11.21q11.23 | 4-6 | 1162;
1163; 1723 |
| 22q13.1q13.33 | 1.0 | 1723 |
| Xp11.23p11.1 | 11.11 | 1733 |
| Xq11.1q13.1 | 45.48 | 1733 |
| Xq13.1q21.1 | 16.76 | 1733 |
| Xq22.1q23 | 3.48 | 1733 |
