04 - January 17, 2013.docx

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Department
Molecular Genetics and Microbiology
Course
MGY299Y1
Professor
Johanna Rommens
Semester
Winter

Description
FINISH LECTURE 03 Human genes and human gene sequencing – other things to pay attention to: sequencing of model organisms with very high degree of accuracy – several organisms started either in parallel with human genome or completed earlier – noted for accuracy that established how to do very good sequencing and complete sequencing – human genome sequence be as accurate as possible – there were surprise: not so many more genes than in model organisms – twenty-thousand genes in C.elegans – protein-coding genes and in humans, twenty to twenty-thousand genes cDNA and transcript sequencing – cDNA sequencing in human genome – people had pushed hard for this because in terms of dollars, RNA is useful information and high information content – push to get all rNA sequenced – inexpensive – fifty-thousand dollars sequence many cDNAs – sequencing cDNA – to get copy of gene AND tag every gene – if can tag gene, can think of every gene at once – ESTs are specific type of STS – useful landmark sequence everything transcribed in cell – projects complement each other some coming from RNA – recognize long non-coding RNA – due to – go through priming step from oligo- DT gets added and this is not true in all RNA in cell – lot sof RNA missed in original cDNA synthesis – coming around that by doing RNA seq technology – will outshine ESTs – newer method – keep track of stage of development of cell type, tissue type – what is transcribed determined by cell type stage of cell – not resolved – moment in time of development of cell that is analyzed – still an issue Benefits and achievements of HGP – Idea of what is an individual is still not addressed TODAY LECTURE Sequences generated from individuals – Ventor from private effort to sequence Multiple emergence from Africa – ot of Africa, through Middle East, India, Australia – from sequence analysis, clear that out of Africa has occurred multiple times, with multiple routes Individual sequences from recent hominin relatives – lots of interesting results Older humans – hominin – difficult to get high-quality DNA – keep in cold and prevent bacterial growth are important to preserve DNA More ancient humans – difficult to find enough high-quality DNA sequences to WGS and WES methods Essentially 90% of genome – involves effort to do this – very intensive bioinformatics analysis Isolate all coding regions and intron-exon boundary segments – amplify what is captured – sequence – by definition – smaller portion of entire genome – approximately 100 of the genome but one price to pay for this rapid sequencing and relatively easier analysis – repetitive sequence gone – faster and easier to manage in terms of data but do not get regulatory and non-coding regions Most of the variation in human genonme is NOT in exons – if want to understand variation in sequence, this method will miss some variation Human genome sequence – recent projects – to capture all common genetic variation – all alleles that occur at one percent frequency – project to capture al lthe diversity – include individuals from all around the world – include some trio families – what is mendelian in terms of sequence variation – individuals have been collected and sequenced – Frances Collins – Criteria at least a hundred and one Improving chromosome maps – New generation chromosome maps – capture breadth of genetic variation – copy number variant information; know alternate sequences (regions in genome like immune response genes that v
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