genome composition
DESCRIPTION
Genome Composition. Loss-Of-function Variants. Group B1 Greg Benz Leo Espinosa David Caro Rupert Wu. Introduction. Loss-of-Function variants The genetic variants predicted to severely disrupt protein- coding genes - PowerPoint PPT PresentationTRANSCRIPT
GENOME COMPOSITIO
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G R O U P B 1G R E G B E N Z L E O E S P I N O S AD A V I D C A R OR U P E R T W U
LOSS-OF-FUNCTIO
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VARIANTS
INTRODUCTION
Loss-of-Function variants
The genetic variants predicted to severely disrupt protein- coding genes
LoF’s include Single-nucleotide variants (SNVs) and insertion/deletion (indel) variants
Recent studies indicates that LoF variants are not always deleterious
Can exist in healthy individual.
Classify the Lof variants:SNVs and indel
Filter the candidate LoF variants into high-confidence , missense and synonymous.
Analyze the numbers and the properties of LoF variants in the individual genome
Filter the candidate LoF variants into high-confidence LoF, missense and synonymous.
Investigate how LoF variants affect human phenotype and disease risk
Some implications of this research:
Predict the probability of disease causation for novel variants.
High confidence LoF:
Mainly include nonsense and frame-shift variants
Usually deleterious.
Missense LoF:
Can not determined.
OVERVIEW OF STUDY
What would we find if our genome was sequenced?
-LoF Variants-Helpful, Harmful, or Harmless?
-Do these variants affect phenotype?
HOW IS THE EFFECT OF GENETIC VARIANCE ON PHENOTYPE SHOWN?
(Quintana-Murci et al. 2012)
DATA (FIGURE 1)
(MacArthur et al. 2012)
DATA (FIGURE 1)
(MacArthur et al. 2012)
DATA (FIGURE 1)
(MacArthur et al. 2012)
DATA (FIGURE 2)
(MacArthur et al. 2012)
DATA (FIGURE 2)
(MacArthur et al. 2012)
DATA (FIGURE 2)
(MacArthur 2012)
DATA (FIGURE 3)
(MacArthur 2012)
DATA (FIGURE 3)
(MacArthur 2012)
DATA (FIGURE 3)
(MacArthur 2012)
DISCUSSION
How does this relate to our Biology class?
Every person has their own unique genomeResult of mutations Different phenotypes3+ billion base pairs in genome
DISCUSSION
Differing base pairs = loss-of-function variantsSingle base change = point mutation
Types of point mutationsSilentMissense Nonsense Frameshift
ACA TGC ATG CCT
Thr Cys Met Pro
Original DNA Sequence
ACG TGC ATG CCT
Thr Cys Met Pro
Silent Mutation
No change in amino acid sequence
ACA TGC ATG CCT
Thr Cys Met Pro
Original DNA Sequence
CCA TGC ATG CCT
Thr Cys Met ProPro
Missense Mutation
Change in one amino acid
ACA TGC ATG CCT
Thr Cys Met Pro
Original DNA Sequence
ACA TGA ATG CCT
Thr Cys Met Pro
Nonsense Mutation
STOPChange from amino acid to stop codon
ACA TGC ATG CCT
Thr Cys Met Pro
Original DNA Sequence
ACA TGC
Thr Ala
Frame Shift
A TC G CC
Thr Cys Met ProChanges in multiple amino acids
Insertion of base C
mRNA
DNA
Transcription
RNA synthesized from DNA template
DISCUSSION
TranslationRNA delivered to ribosomesEach codon aligns with its anticodonAmino acid produced for each codonAmino acids joined by peptide bonds to form a polypeptide (protein)
TAKE-HOME MESSAGE
“Everyone’s Got Problems”
REFERENCESMacarthur, Daniel G. . "A Systematic Survey of Loss-of-Function Variants in
Human Protein-Coding Genes ." Science 335 (2012): 823-828. Print. Quintana-Murci, Lluis. "Gene Losses in the Human Genome." Science 14
Nov. 2012: 806-807. Print.Freeman, Scott, and Healy Hamilton. Biological science. 4th ed. Upper
Saddle River, N.J.: Pearson Prentice Hall, 2011. Print.Segalat, Laurent. "Loss-of-function Genetic Diseases and the Concept of
Pharmaceutical Targets ." Orphanet 225 (2007): Web. 18 Nov. 2012