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About classical molecular genetics, cytogenetic and molecular cytogenetic data not considered by Genome Reference Consortium and thus not included in genome browsers like UCSC, Ensembl or NCBI
Molecular Cytogenetics ( IF 1.3 ) Pub Date : 2021-03-20 , DOI: 10.1186/s13039-021-00540-7
Thomas Liehr

The Genome Reference Consortium (GRC) has according to its own statement the “mission to improve the human reference genome assembly, correcting errors and adding sequence to ensure it provides the best representation of the human genome to meet basic and clinical research needs”. Data from GRC is included in genome browsers like UCSC (University of California, Santa Cruz), Ensembl or NCBI (National Center for Biotechnology Information) and are thereby bases for scientific and diagnostically working human genetic community. Here long standing knowledge deriving from classical molecular genetic, cytogenetic and molecular cytogenetic data, not being considered yet by GRC was revisited. There were three major points identified: (1) GRC missed to including three chromosomal subbands, each, for 1q32.1, 2p21, 5q13.2, 6p22.3 and 6q21, which were defined by International System for Human Cytogenetic Nomenclature (ISCN) already back in 1980s; instead GRC included additional 6 subbands not ever recognized by ISCN. (2) GRC defined 34 chromosomal subbands of 0.1 to 0.9 Mb in size, while it is general agreement of cytogeneticists that it unlikely to detect chromosomal aberrations below 1–2 Mb in size by GTG-banding. And (3): still all sequences used in molecular cytogenetic routine diagnostics to detect heterochromatic and/ or pericentromeric satellite DNA sequences within the human genome are not included yet into human reference genome. For those sequences, localization and approximate sizes have been determined in the 1970s to 1990, and if included at least ~ 100 Mb of the human genome sequence could be added to the genome browsers. Overall, taking into account the here mentioned points and correcting and including the data will definitely provide to the still not being completely finished mapping of the human genome.

中文翻译:

关于经典分子遗传学,基因组参考协会未考虑并因此未包含在基因组浏览器(如UCSC,Ensembl或NCBI)中的细胞遗传学和分子细胞遗传学数据

Genome Reference Consortium(GRC)根据其自己的陈述“有责任改善人类参考基因组的装配,纠正错误和增加序列,以确保其能最好地代表人类基因组,从而满足基础和临床研究的需求”。GRC的数据包含在基因组浏览器中,例如UCSC(加利福尼亚大学圣克鲁斯分校),Ensembl或NCBI(国家生物技术信息中心),因此是人类基因界进行科学和诊断工作的基础。在这里,人们回顾了长期以来从经典分子遗传学,细胞遗传学和分子细胞遗传学数据中获得的知识,而GRC尚未考虑这些知识。确定了三个主要点:(1)GRC缺少三个染色体子带,每个子带分别用于1q32.1、2p21、5q13.2、6p22.3和6q21,早在1980年代,国际人类细胞遗传命名系统(ISCN)就对其进行了定义;相反,GRC包含ISCN从未认识到的其他6个子带。(2)GRC定义了34个大小为0.1到0.9 Mb的染色体子带,而细胞遗传学家普遍同意,它不太可能通过GTG频带检测到小于1-2 Mb的染色体畸变。(3):分子细胞遗传学常规诊断中用于检测人类基因组中异色和/或着丝粒卫星DNA序列的所有序列仍未包括在人类参考基因组中。对于那些序列,已在1970年代至1990年确定了定位和近似大小,如果包括在内,则可以将至少约100 Mb的人类基因组序列添加到基因组浏览器中。全面的,
更新日期:2021-03-21
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