Improved accuracy assessment for 3D genome reconstructions

BMC Bioinformatics
Mark R Segal, Henrik Bengtsson

Abstract

Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome conformation had been difficult to elucidate but the advent chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin architecture and yielded numerous biological insights. Although most of these findings have flowed from analysis of proximity data produced by these assays, added value in generating 3D reconstructions has been demonstrated, deriving, in part, from superposing genomic features on the reconstruction. However, advantages of 3D structure-based analyses are clearly conditional on the accuracy of the attendant reconstructions, which is difficult to assess. Proponents of competing reconstruction algorithms have evaluated their accuracy by recourse to simulation of toy structures and/or limited fluorescence in situ hybridization (FISH) imaging that features a handful of low resolution probes. Accordingly, new methods of reconstruction accuracy assessment are needed. Here we utilize two recently devised assays to develop methodology for assessing 3D reconstruction accuracy. M...Continue Reading

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Citations

Feb 26, 2020·BMC Bioinformatics·Mark R Segal, Kipper Fletez-Brant
Nov 23, 2020·Biostatistics·Elena TuzhilinaMark R Segal

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Datasets Mentioned

BETA
GSE35156
GSE64881

Methods Mentioned

BETA
ChIP-Seq
Hi-C
single-cell Hi-C
GAM

Software Mentioned

Procrustes
R
HSA
R package vegan
GAM
FisHiCal

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