Translocation detection from Hi-C data via scan statistics.
Biometrics
; 79(2): 1306-1317, 2023 06.
Article
in En
| MEDLINE
| ID: mdl-35861170
ABSTRACT
Recent Hi-C technology enables more comprehensive chromosomal conformation research, including the detection of structural variations, especially translocations. In this paper, we formulate the interchromosomal translocation detection as a problem of scan clustering in a spatial point process. We then develop TranScan, a new translocation detection method through scan statistics with the control of false discovery. The simulation shows that TranScan is more powerful than an existing sophisticated scan clustering method, especially under strong signal situations. Evaluation of TranScan against current translocation detection methods on realistic breakpoint simulations generated from real data suggests better discriminative power under the receiver-operating characteristic curve. Power analysis also highlights TranScan's consistent outperformance when sequencing depth and heterozygosity rate is varied. Comparatively, Type I error rate is lowest when evaluated using a karyotypically normal cell line. Both the simulation and real data analysis indicate that TranScan has great potentials in interchromosomal translocation detection using Hi-C data.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Translocation, Genetic
/
Chromosomes
Type of study:
Diagnostic_studies
Limits:
Humans
Language:
En
Journal:
Biometrics
Year:
2023
Document type:
Article
Affiliation country:
Estados Unidos