scholarly journals GENCODE: The reference human genome annotation for The ENCODE Project

2012 ◽  
Vol 22 (9) ◽  
pp. 1760-1774 ◽  
Author(s):  
J. Harrow ◽  
A. Frankish ◽  
J. M. Gonzalez ◽  
E. Tapanari ◽  
M. Diekhans ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Annotation ◽  
Encode Project ◽  
Reference Human Genome

Towards the Human Cancer Genome Project: A Sequence-Ready Physical Map of a Follicular Lymphoma Genome.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 605-605
Author(s):  
Marco A. Marra ◽  
Martin Krzywinski ◽  
Readman Chiu ◽  
Matthew Field ◽  
Inanc Birol ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
Human Genome ◽  
Large Scale ◽  
Reference Genome ◽  
Reference Sequence ◽  
Whole Genome ◽  
Bac Clones ◽  
Genome Maps ◽  
Tumor Genome ◽  
Reference Human Genome

Abstract With the aim of identifying and sequencing mutations in follicular lymphoma genomes, we have begun a project to generate at least 24 deeply redundant sequence-ready Bacterial Artificial Clone (BAC) - based whole genome maps, each from a different individual’s lymphoma. BAC-array CGH and Affymetrix whole-genome sampling assays (WGSA) will be used along with the mapping data to identify genomic amplifications and losses in the lymphomas. Results from the mapping and array studies will be used to prioritize BAC clones for sequence analysis. Because each map will span essentially the entire genome of the corresponding lymphoma, we anticipate that essentially all regions of each tumor genome will be represented in easily sequenced BAC clones. This approach facilitates targeted sequencing of genomic regions of interest, including those containing genes relevant to cancer or harboring amplifications or deletions. Our mapping strategy hinges on the successful creation of deeply redundant high quality BAC libraries from primary lymphomas and large scale high throughput restriction enzyme fingerprinting of individual BACs with a version of the technology we used to map the human, mouse, rat and other genomes. The effort is large-scale, and will result in the generation of at least 2.5 million fingerprinted BAC clones over the next three years. Using the fingerprints, we will align the BACs to the reference human genome to assess genome coverage and to identify candidate genome rearrangements. In parallel, we will assemble the fingerprints into genome maps, looking for larger-scale genome variations between the lymphoma maps and the reference genome sequence. To test the feasibility of our approach, we obtained two restriction digest fingerprints from each of 140,000 individual BAC clones. BACs were sampled from a 7-fold redundant BAC library that had been created from genomic DNA purified from a primary follicular lymphoma sample. The fingerprints are being assembled into a clone map with the intent of reconstructing the entire tumor genome. 90,377 fingerprinted clones with unambiguous single alignments to the reference sequence were automatically assembled into 15,538 contigs. Subsequent rounds of semi-automatic contig merging further reduced the number of contigs to 5,433. Only 1,241 clones remained unassembled. We anchored the tumor genome map to the reference human genome sequence by aligning the clone fingerprints to the restriction map computed from the reference sequence assembly. As a result of this, we identified a BAC that captured the canonical t(14;18) translocation characteristic of follicular lymphomas. We sequenced this BAC and confirmed that it contains the expected translocation. Almost 2.6 gigabases (~91%) of the reference genome are represented in the evolving map, with an additional 50,000 clone fingerprints awaiting incorporation into the map assembly. Among these are repeat-rich and other clones that may well harbor genome rearrangements. Additional prioritization of sequencing targets will be undertaken when map construction and analysis of genome copy number alterations are complete.

scholarly journals The Need for a Human Pangenome Reference Sequence

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Karen H. Miga ◽  
Ting Wang
Keyword(s):  
Human Genome ◽  
Genome Sequence ◽  
Human Genetics ◽  
Genomic Diversity ◽  
Human Genome Sequence ◽  
Reference Sequence ◽  
Annual Review ◽  
Publication Date ◽  
Reference Structure ◽  
Reference Human Genome

The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Assessing the impact of human genome annotation choice on RNA-seq expression estimates

2013 ◽  
Vol 14 (Suppl 11) ◽  
pp. S8 ◽  
Author(s):  
Po-Yen Wu ◽  
John H Phan ◽  
May D Wang
Keyword(s):  
Human Genome ◽  
Genome Annotation ◽  
Rna Seq ◽  
The Impact

scholarly journals Myosin-I nomenclature

2001 ◽  
Vol 155 (5) ◽  
pp. 703-704 ◽  
Author(s):  
Peter G. Gillespie ◽  
Joseph P. Albanesi ◽  
Martin Bähler ◽  
William M. Bement ◽  
Jonathan S. Berg ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Organization ◽  
Genome Annotation ◽  
Nomenclature System ◽  
Myosin I

We suggest that the vertebrate myosin-I field adopt a common nomenclature system based on the names adopted by the Human Genome Organization (HUGO). At present, the myosin-I nomenclature is very confusing; not only are several systems in use, but several different genes have been given the same name. Despite their faults, we believe that the names adopted by the HUGO nomenclature group for genome annotation are the best compromise, and we recommend universal adoption.

scholarly journals Human genome annotation — a possible role for HUGO?

10.1038/896 ◽  
1998 ◽  
Vol 19 (3) ◽  
pp. 222-222 ◽  
Author(s):  
Peter Little
Keyword(s):  
Human Genome ◽  
Genome Annotation
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