14 Genomes

genome

DNA in haploid set of chromosomes

genomics

study of genomes

cytogenetic map

highlights largest cities like map of Cali in US

Linkage map

depicts smaller cities and large towns

physical map

similar to geographical map indicating towns in area

sequence map

google map showing all buildings in specific town

human genome project

idea to sequence human genome in 1980s under DOE and NIH; draft in 2001; finished sequence in 2003

sequencing genome

clone-by-clone approach (align pieces one chromosome at a time); Celera Genomics uses whole genome shotgun approach (shatter genome and rebuild)

1. Sequencing: DNA shot gunned into small fragments using restriction enzymes; sequencer devices sequence the fragments

2. Assembly: Software aligns ends of DNA pieces by recognizing overlaps

deriving DNA sequence

Gene Annotation

description of gene function and significance of likely gene variant; mode of inheritance; genotype; frequency of variance; classification (benign/pathogenic)

human genome content

1.5% of DNA encodes proteins; at end of genome project (2003) 95% protein encoding genes IDd; Viral DNA, noncoding RNA, introns, promoters, control and repeated sequences do not encode protein

exome

sequenced telomere-to-telomere in chromosomes; repeats and reveals structural variants

transcriptome

set of RNA transcripts (coding/noncoding)

Which sequencing technology would be most appropriate for identifying

mutations in protein-coding regions of the genome?

A. RNA sequencing

B. Whole genome sequencing

C. Exome sequencing

D. Single cell sequencing

C. Exome sequencing

A researcher wants to study the differences in gene expression between

cancerous and normal cells. Which NGS method would be most suitable?

A. Whole genome sequencing

B. Exome sequencing

C. Single-cell sequencing

D. RNA sequencing

D. RNA sequencing

If you want to specifically study alternative splicing events in a transcriptome,

which NGS technology would you prefer?

A. Whole genome sequencing

B. Exome sequencing

C. Single-cell sequencing

D. RNA sequencing

D. RNA sequencing

viral DNA

8% of genome from RNA viruses [RETROVIRUSES]; evidence of past infection; sequences increase over time; genetic material in chromosomes is '“human endogenous retroviruses (HERVs)”

HERV sequences have recombines/exchanged parts and mutated to not make us sick; AML, MS, and melanoma are overexpressed HERVs

noncoding RNA

genome transcribed in form of ncRNAs (all RNA except mRNA); transcribed from pseudogenes

tRNAs: connect mRNA codons to amino acids; ~500 tRNA genes are 0.1% of genome

rRNAs: ribosome parts; 243 types grouped on 6 chromosomes

12000 long noncoding RNAs: >200 nucleotides, transcribed from exons introns and between gene regions (chromatin and gene expression control), 1/3 in primates only, most in brain

repeats

highly repetitive sequences holding diff type of information than protein’s amino acid sequence; transposons are most abundant type of repeat; rare classes include telomeres, centromeres, and pseudogenes

transposons

jumping sequences; Alu repeats can copy themselves and comprise of 2-3% of genome

Large intergenic noncoding RNAs

Between genes

Small nucleolar RNAs (snoRNAs)

Process rRNAs in nucleolus

Small nuclear RNAs (snRNAs)

Parts of spliceosomes

Telomerase RNA

Adds bases to chromosome tips

Xist RNA

Inactivates one X chromosome in cells of

females

introns

genes cut out of mRNA

Promoters and other control

sequences

Guide enzymes that carry out DNA replication,

transcription, or translation

Small interfering RNAs (siRNAs)

MicroRNAs (miRNAs)

control translation

circular RNA

degrades microRNA, mostly in synapses

centromeres

Largest constrictions in chromosomes, providing

attachment points for spindle fibers

genomic medicine

breast cancer - tests for 3 mutations in BRCA1/BRCA2

breast cancer gene test panel - tests for variants/complete sequences of >100 genes

genome editing

restriction endonucleases to cut and paste DNA molecules in patterns; used on somatic/germline cells; techniques include ZFNs (zinc finger nuclease), TALENs (Transcription-activator-like effector nucleases), and CRISPR-Cas9 (Clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9)