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The Human Chromosomes

The Human Chromosomes. 1. Other Structural Variants. Inversion. Deletion. Copy number variant. Other mutations - recombination. Copy 1. Copy 2. Probability r i (~10^-8) for recombination in position i. child chromosome. The Vision of Personalized Medicine.

sean-blackburn
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The Human Chromosomes

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  1. The Human Chromosomes 1

  2. Other Structural Variants Inversion Deletion Copy number variant

  3. Other mutations - recombination Copy 1 Copy 2 Probability ri (~10^-8) for recombination in position i. child chromosome

  4. The Vision of Personalized Medicine Genetic and epigenetic variants + measurable environmental/behavioral factors wouldbe used for a personalized treatment and diagnosis

  5. Association Studies Genetic variants such as Single Nucleotide Polymorphisms (SNPs), Copy Number Variants (CNVs) are tested for association with the trait.

  6. Where should we look? Associated SNP Usually SNPs are bi-allelic SNP= Single Nucleotide Polymorphism Cases: AGAGCAGTCGACAGGTATAGCCTACATGAGATCGACATGAGATCGGTAGAGCCGTGAGATCGACATGATAGCC AGAGCCGTCGACATGTATAGTCTACATGAGATCGACATGAGATCGGTAGAGCAGTGAGATCGACATGATAGTC AGAGCAGTCGACAGGTATAGTCTACATGAGATCGACATGAGATCGGTAGAGCCGTGAGATCGACATGATAGCC AGAGCAGTCGACAGGTATAGCCTACATGAGATCAACATGAGATCGGTAGAGCAGTGAGATCGACATGATAGCC AGAGCCGTCGACATGTATAGCCTACATGAGATCGACATGAGATCGGTAGAGCCGTGAGATCAACATGATAGCC AGAGCCGTCGACATGTATAGCCTACATGAGATCGACATGAGATCGGTAGAGCAGTGAGATCAACATGATAGCC AGAGCCGTCGACAGGTATAGCCTACATGAGATCGACATGAGATCGGTAGAGCAGTGAGATCAACATGATAGTC AGAGCAGTCGACAGGTATAGCCTACATGAGATCGACATGAGATCTGTAGAGCCGTGAGATCGACATGATAGCC Controls: AGAGCAGTCGACATGTATAGTCTACATGAGATCGACATGAGATCGGTAGAGCAGTGAGATCAACATGATAGCC AGAGCAGTCGACATGTATAGTCTACATGAGATCAACATGAGATCTGTAGAGCCGTGAGATCGACATGATAGCC AGAGCAGTCGACATGTATAGCCTACATGAGATCGACATGAGATCTGTAGAGCCGTGAGATCAACATGATAGCC AGAGCCGTCGACAGGTATAGCCTACATGAGATCGACATGAGATCTGTAGAGCCGTGAGATCGACATGATAGTC AGAGCCGTCGACAGGTATAGTCTACATGAGATCGACATGAGATCTGTAGAGCCGTGAGATCAACATGATAGCC AGAGCAGTCGACAGGTATAGTCTACATGAGATCGACATGAGATCTGTAGAGCAGTGAGATCGACATGATAGCC AGAGCCGTCGACAGGTATAGCCTACATGAGATCGACATGAGATCTGTAGAGCCGTGAGATCGACATGATAGCC AGAGCCGTCGACAGGTATAGTCTACATGAGATCAACATGAGATCTGTAGAGCAGTGAGATCGACATGATAGTC

  7. Genome-Wide Association Studies High-throughput genotyping technologiesallow for the genotyping of millions of variants for thousands of individuals

  8. Two minute genetic primer • Recombining DNA: • Chromosome we get from each parent is mixture of both their copies • Every base pair can have different inheritance history • Non-recombining DNA: • Mitochondrial (mtDNA) maternally inherited • Most Y chromosome (NRY) in men paternally inherited Non-recombining DNA has unique inheritance history. In particular, there is a unique mtDNA family tree and a unique NRY family tree on which we all sit: NRY-Adam lived about 60K years ago in Africa mtDNA-Eve lived about 150K years ago in Africa Inheritance Trees

  9. Example of conclusion: my story My background: Ashkenazi Jewish on all sides My family name: Rosset, Western-European non-Jewish sounding Question: which is my paternal heritage story? Answer: I belong to Y-haplogroup J2, which is very common among Jews, very rare in Western Europe • Confirms family story, family name still a mystery

  10. Example of conclusion: Genghis Khan’s Y? Investigating populations throughout East and Central Asia, investigators discovered 8% of men had VERY closely related Y chromosome Suggests common ancestor within 1000 years Obvious candidate: Genghis Khan and his male progeny Verifying conclusion: • This lineage had greatest diversity in Mongolia (indicates origin) • Had higher prevalence among Hazara in Pakistan, who have oral tradition of being Genghis Khan’s descendents

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