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| Status |
Public on Nov 15, 2022 |
| Title |
CRISPR-based targeted haplotype-resolved assembly of a megabase region [WGBS] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
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| Overall design |
10x linked-reads, CCS reads and WGBS for Enriched MHC, RNA-seq sequencing and Illumina Human Methylation 850 BeadChip for NA12878
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| Contributor(s) |
Li T, Du D, Zhang D |
| Citation(s) |
36596772 |
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| Submission date |
Dec 22, 2021 |
| Last update date |
Jan 06, 2023 |
| Contact name |
Yun Liu |
| E-mail(s) |
yliu39@fudan.edu.cn
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| Organization name |
Fudan University
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| Street address |
130 Dong An Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platforms (1) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE192502 |
CRISPR-based targeted haplotype-resolved assembly of a megabase region |
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| Relations |
| BioProject |
PRJNA791667 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE192499_RAW.tar |
5.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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