6. Genome Sequencing Today

Which statements regarding segmental duplications (Sds) are correct?

1) ~5% of the human genome falls in Sds

2) Segmental duplications are by definition two copies of DNA only

3) Sds are enriched close to telomeres and close to centromers

4) Segmental duplications are DNA regions with >1kbp in length and >90% sequence similarity that occur at least twice in the genome

5) Sds are a major reason why long read technologies increase the quality of genome assemblies

Which statements regarding de novo genome sequencing are correct?

1) A genome with longer and more similar repeats is more difficult to assemble

2) Hi-C is a technology that uses Illumina sequencing

3) The quality (N50 contig length) of a human genomse assembly approximately doubles when the coverage of Illumina reads is increased from 50x to 100x

4) A 50x Oxford Nanopore assembly is better than the current Human Reference Genome

5) A de Brujin graph is a computational framwork used for genome assemblies

Which statements regarding resequencing of human genomes are true?

1) Resequencing requires a reference genome

2) 30x coverage is a current standard for sequencing and genotyping a single individual

3) At a site with 4x coverage, the change that only one of two alleles has been sequenced is 6.25%

4) If 10% of all cancer cells in a pure cancer sample carry a heterozygous mutation that makes them therapy resistant, the chance to not sequence this mutation at a 30x coverage is 0.95^30 = 21.5% (assuming diploid cells)

Which statements regarding exome sequencing are correct?

1) For exome sequencing, genomic DNA is usually hybridized to probes that are complementary to exnic sequences

2) No reference genome is required for exome sequencing

3) In contrast to whole genome resequencing, exome sequencing allows detecting genetic variants in protein coding genes

4) Exome sequencing is a cost efficient alternative to whole genome re-sequencing

5) Exome sequencing is usually done by PCR amplification of all exons

Which statements regarding the sacle of current genome sequencing are correct?

1) Most sequenced human genomes today are de novo assemblies

2) The current release of the International Cancer Atlas Consortium contains over 20000 donors

3) The 1000 Genomes project has been completed in 2015 by sequencing 2500 people from populations around the world

4) The vertebrate genome project has just published de novo assemblies of 70000 vertebrates

5) GnomAD is a consortium that has compiled whole exome sequences from over 100 000 cancer genomes