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人类 diplome 的探究:计算方法、新兴应用和挑战。

Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges.

机构信息

The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA.

Courant Institute of Mathematical Sciences at New York University, New York, NY, USA.

出版信息

Methods Mol Biol. 2023;2590:1-30. doi: 10.1007/978-1-0716-2819-5_1.


DOI:10.1007/978-1-0716-2819-5_1
PMID:36335489
Abstract

Human DNA sequencing protocols have revolutionized human biology, biomedical science, and clinical practice, but still have very important limitations. One limitation is that most protocols do not separate or assemble (i.e., "phase") the nucleotide content of each of the maternally and paternally derived chromosomal homologs making up the 22 autosomal pairs and the chromosomal pair making up the pseudo-autosomal region of the sex chromosomes. This has led to a dearth of studies and a consequent underappreciation of many phenomena of fundamental importance to basic and clinical genomic science. We discuss a few protocols for obtaining phase information as well as their limitations, including those that could be used in tumor phasing settings. We then describe a number of biological and clinical phenomena that require phase information. These include phenomena that require precise knowledge of the nucleotide sequence in a chromosomal segment from germline or somatic cells, such as DNA binding events, and insight into unique cis vs. trans-acting functionally impactful variant combinations-for example, variants implicated in a phenotype governed by compound heterozygosity. In addition, we also comment on the need for reliable and consensus-based diploid-context computational workflows for variant identification as well as the need for laboratory-based functional verification strategies for validating cis vs. trans effects of variant combinations. We also briefly describe available resources, example studies, as well as areas of further research, and ultimately argue that the science behind the study of human diploidy, referred to as "diplomics," which will be enabled by nucleotide-level resolution of phased genomes, is a logical next step in the analysis of human genome biology.

摘要

人类 DNA 测序方案彻底改变了人类生物学、生物医学科学和临床实践,但仍存在非常重要的局限性。其中一个限制是,大多数方案无法分离或组装(即“相”)构成 22 对常染色体和性染色体假常染色体区域的母源和父源染色体同源物的核苷酸含量。这导致对许多对基础和临床基因组科学至关重要的现象缺乏研究和相应的认识。我们讨论了几种获取相信息的方案及其局限性,包括可用于肿瘤相分析的方案。然后,我们描述了一些需要相信息的生物学和临床现象。这些现象包括需要从生殖细胞或体细胞中精确了解染色体片段中的核苷酸序列的现象,例如 DNA 结合事件,以及深入了解独特的顺式与反式作用功能有影响的变异组合的能力,例如与由复合杂合性控制的表型相关的变异。此外,我们还评论了对基于变异识别的可靠共识二倍体背景计算工作流程的需求,以及对基于实验室的功能验证策略的需求,以验证变异组合的顺式与反式效应。我们还简要描述了可用资源、示例研究以及进一步研究的领域,并最终认为,通过对相基因组进行核苷酸水平解析,研究人类二倍体的背后科学,即“二倍体组学”,将是人类基因组生物学分析的合乎逻辑的下一步。

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引用本文的文献

[1]
The human pangenome reference anticipates equitable and fundamental genomic insights.

Cell Genom. 2023-7-12

本文引用的文献

[1]
Recent advances in therapeutic nucleic acids and their analytical methods.

J Pharm Biomed Anal. 2021-11-30

[2]
Systematic Evaluation of DNA Sequence Variations on Transcription Factor Binding Affinity.

Front Genet. 2021-9-9

[3]
Protein-coding repeat polymorphisms strongly shape diverse human phenotypes.

Science. 2021-9-24

[4]
The Role of Neoantigens in Cancer Immunotherapy.

Front Oncol. 2021-8-27

[5]
Blood-Brain Barrier, Cell Junctions, and Tumor Microenvironment in Brain Metastases, the Biological Prospects and Dilemma in Therapies.

Front Cell Dev Biol. 2021-8-24

[6]
Nucleic acid delivery for therapeutic applications.

Adv Drug Deliv Rev. 2021-11

[7]
SpecHap: a diploid phasing algorithm based on spectral graph theory.

Nucleic Acids Res. 2021-11-8

[8]
In silico saturation mutagenesis of cancer genes.

Nature. 2021-8

[9]
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA.

Nat Biotechnol. 2021-12

[10]
Shifting landscapes of human MTHFR missense-variant effects.

Am J Hum Genet. 2021-7-1

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