The Human Genome Project (HGP) Lecture

The Human Genome Project (HGP) Lecture Molecular Biology Revolution 1907 Genetics – study of inheritance from one generation to another, how people get traits 1953 – DNA's double helix that proved this idea of genetics 1987 – creation of field of Genomics ● Complete study of a genome/DNA and how it works Technology used to study DNA of bits of pieces 1970s: DNA cloning to study bits of pieces of DNA 1977: DNA sequencing 1983: Polymerase Chain reaction (PCR) selecting certain parts of DNA Technology at an increased efficiency and a larger scale 1980s: editorals, scientist commentaries, new journal, government got involved, congressional hearings and money came in to start the project Original Plan of The HGP 1990 1. 15-year project (Took 13 years) 2. First start with other smaller genomes and studied heavily (Model Genomes) to then start on the human genome a. Studied Humans, Mouse, Fruit Fly & Nematoda, Yeast i. Picked heavily studied organisms but also spread out across the revolutionary tree ii. Created books to conceptualize genomes (books with list of the human genome sequence) 3. Map the DNA to organize THEN sequence to read 4. Must need new revolutionary DNA sequencing methods to develop to replace Sanger DNA sequencing a. Wasn't accomplished 5. The primary goal was to generate the first sequence of the human genome a. Was accomplished What didn’t exist for the HGP 1990 Wanted to read 3 billion bp (base pairs) in the human genome, but it was a large task due to the low technology ● Webpages, texting, live streaming, web browsing, consoles, GPS, social media, WIFI, google, DVDs, USB cables Realities of 1990 HGP Launch ● ● ● ● Scientific community had concerns for his importance and results No detailed plan to accomplish this goal No specific trained genomics field person No internet, so used books/papers or CDs or fax machine to write up and distribute the genome sequence data Implementation of HGP ● International project: received funding from NIH, DOE, and from other countries from some government and private funders ● Team science effort ● Periodically updated scientific plans for each part of HGP, frequently updated Genomes Organized by Chromosomes ● Found in living organisms & varies in size/scale ● Human genome ~3,000 Mb – Human Chromosome ~ 130 Mb (entire fruit fly genome) Clone-Based Physical Mapping ● Chromosome is cloned to organize and isolate bits of DNA ● Clones Contigs (continuous region): overlapped to find similarities page by page to represent a fragment of the genome to organize and map the DNA ○ Imperfect since books have page breaks so not perfect overlapping Shotgun Sequencing ● Determines the DNA sequence of the organism's genome ● Randomly breaks the DNA into small fragments ● Looks for overlaps in the DNA sequences to resemble the fragments in correct order Generating DNA Sequence Read ● Clone DNA turned into Subcloned DNA fragments are put through a Sanger DNA sequencing instrument thousands of times ○ To create enough redundancy to resemble them altogether in an accurate way to read it over and over (coverage) ● Clone DNA to Subclones to generate shotgun sequence reads to assemble them into sequence Contigs to deduce sequence to working draft sequence to final Sequence Assembly Challenge: Repeated Sequences ● Similar fragments that are confused for one another First Eukartotic Genomes Sequenced by HGP: Yeast, Worm, Fly Challenges of Sequencing Human Genome ● ~3,000,000,000 nucleotides and “coverage” of 4 times each ● Sanger DNA sequencing in 1990 could only read 500-700 each time ○ Scaled up the sequence for automation and used computational power to feed data in and put it together and involved many countries ○ 70% blood used was from 1 person, 30% from 19 other people ○ “mosaic” representation of multiple people, served as a “reference” Bermuda Principles for Data Sharing in 1997 ● DNA sequence data would be shared HGP Drama ● Francis Collins & Craig Venter: created company, Venter/Celera Genomics, raced the HGP to generate the Human genome sequence and patented genes ○ Wanted to have computer sequence whole genome ○ Had access to all HGP data, but not vice versa ● 2000: president stated it was a tie to defuse ● 2001: Draft Sequence of Human Genome ● HGP focused on improving draft, but Celera’s got lazy and didn’t want to ● HGP merged the 2 different plans to finish in 2003 Highlights ● Completed in 13 years (not 15) and underbudget 1990-2003 ● Primary accomplishment: quality sequence of ~92% of human genome ○ 8% left were very repeatable & structural difficult ○ New methods for better computation made a complete sequence in 2023 ○ Millions of other human genomes have been sequenced since ● Race was defused in 2000 and controversial ● Set of fields of genomes became widespread in other scientific fields ● Used a Map-first, sequence-second ○ Sanger DNA sequencing (not revolutionary) which made it difficult due to its large scale and repeat regions