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CSE 180: summary

Yana Safonova

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Sequencing data

Illumina

Long-read technologies (PacBio, Nanopore)

Short-read long-distance reads (10x, Hi-C)

Whole Genome Sequencing

Whole Exome Sequencing

RNA-Seq

Target sequencing

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Sequencing data

Illumina

Long-read technologies (PacBio, Nanopore)

Short-read long-distance reads (10x, Hi-C)

Whole Genome Sequencing

Whole Exome Sequencing

RNA-Seq

Target sequencing

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Sequencing data

Illumina

Long-read technologies (PacBio, Nanopore)

Short-read long-distance reads (10x, Hi-C)

Whole Genome Sequencing

Whole Exome Sequencing

RNA-Seq

Target sequencing

Read assembly

Alignment to reference

De novo gene prediction

Differential gene expression

Haplotype assembly

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Sequencing data

Illumina

Long-read technologies (PacBio, Nanopore)

Short-read long-distance reads (10x, Hi-C)

Whole Genome Sequencing

Whole Exome Sequencing

RNA-Seq

Target sequencing

Read assembly

Population studies / comparative genomics

Meta-

genomics

Alignment to reference

De novo gene prediction

Differential gene expression

Haplotype assembly

Genomics

Transcriptomics

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Rep-seq: special type of RNA-seq data

B and T cells produce special types of receptors that are not encoded in the original (germline genome)

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Antibodies are agents of the adaptive immune system

  • Antibodies are proteins that bind to an antigen and cause its neutralization

​

  • Antibodies are not encoded in the genome directly, but present a result of somatic genomic recombination

V

V

V

D

D

D

J

J

D

chr 14

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Antibodies are agents of the adaptive immune system

  • Diversity of antibody genes is extremely high
  • Set of produced antibodies (antibody repertoire) is unique for an individual
  • Antibodies are proteins that bind to an antigen and cause its neutralization

​

  • Antibodies are not encoded in the genome directly, but present a result of somatic genomic recombination

V

V

V

D

D

D

J

J

D

chr 14

J

D

V

V

J

antibody gene

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Antibodies are subjects of fast evolution

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Immune system mutates and amplifies a binding antibody

Mutation rate in antibody genes is 3-4 order of magnitude higher than in other genome

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One antibody = one antigen

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Antibody repertoire is a set of clonal lineages

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Antibody repertoire is a set of unknown clonal lineages

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Application of Rep-seq data

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Healthy individual

Flu vaccination

HIV donor

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Proteomics

  • Quantitative proteomics
  • Protein sequencing
  • Drug design

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Large sequencing projects

Genomics

Transcriptomics

Metagenomics

(microbiome)

Repertoire sequencing

Proteomics

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Phylogenetics

HIV

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Protein folding

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Protein binding

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Bioinformatics is not limited by analysis of sequences

karyotyping

finding non-chromosomal DNAs