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1. Introduction
2. Long term goals for genotype-phenotype studies
3. Reference article
4. Overview
5. De novo genome assembly (1)
6. De novo genome assembly (2)
7. HuRef compared to other human assemblies
8. HuRef vs. NCBI
9. Celera assembler
10. The variants detected
11. The filtering approach
12. Identification of a comprehensive HuRef variant set
13. SNP in HuRef assembly
14. Detecting allelic contributions for SNP and indels
15. How do variants impact coding sequence?
16. Measure of nucleotide diversity
17. Characterization of indels
18. Homozygous insertions and deletions
19. Zinc finger protein truncated by 467 bp insertion
20. Analysis of insertions and deletions
21. CNVs and read depth coverage
22. Characterization of novel HuRef sequences
23. Building long range haplotypes
24. Haplotype assembly
25. Increasing HuRef coverage with ABI SOLiD data
26. 2 assembly approaches employing additional data
27. Mapping and pairing of reads from ABI-SOLiD runs
28. Improving accuracy of SNP detection
29. SNPs are missed due to reasons of coverage
30. Mapping parameters are important for accuracy
31. Identifying large insertions
32. Small length mate-pairs confirm known insertions
33. Concluding remarks
34. Contributions (1)
35. Contributions (2)

Topics Covered

• Long term goals for human genotype-phenotype studies
• De novo assembly of an individual genome sequence
• How does HuRef compare to other human assemblies?
• SNP in HuRef assembly
• How do variants impact coding sequence?
• Nucleotide diversity
• Homozygous insertions and deletions: identification and validation
• CNVs and read depth coverage
• Construction of haplotypes and diploid representation
• Additional sequencing to provide complete genome assembly through detection of indels/CNV

Links

Series:

• Copy Number Variation

Categories:

• Genetics & Epigenetics

Talk Citation

Levy, S. (2009, August 30). Indels, CNVs and the spectrum of human genome variation [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved April 15, 2025, from https://doi.org/10.69645/OHRF7802.
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Publication History

• Published on August 30, 2009
• Archived on February 25, 2021

Financial Disclosures

• Prof. Samuel Levy has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.