Incoming Data QC and our ability to detect commonly
`known genetic diseases
`
`Personalis EX2115.1
`
`
`known genetic diseases
`
`Personalis EX2115.1
`
`
`
`SOME WELL KNOWN MENDELIAN DISEASES
`
`Albinism
`
`Becker Muscular Dystrophy
`Beta Thalassemia
`
`Canavan Disease
`
`Charcot-Marie-Tooth Disease
`
`Creutzfeldt-Jacob Disease
`
`Cystic Fibrosis
`Down Syndrome
`Duchenne Muscular Dystrophy
`Fabry Disease
`Factor ¥ Leiden
`
`Familial Adenomatous Polyposis
`Familial Alzheimer Disease
`
`Fragile X syndrome
`Gaucher Disease
`Haemophilia (A&B)
`Hemochromatosis
`
`Huntington's
`Hypertrophic Cardiomyopathy
`Long OT Syndrome
`Marfan Syndrome
`Paget Disease
`Phenylketonuria
`Pompe Disease
`Retinitis Pigmentosa
`Sickle Cell Anemia
`
`Stargardt Disease
`Tay-Sachs Disease
`Thrombocytopenia
`
`Lin 17,000 per Wikipedia
`3-6 of 100,000 per Wikipedia
`Rates vary enormously by geography, but some poapul;
`Lin 40 of Ashkenazi Jewish background
`36 per 100,000 per Wikipedia
`1 per million per Wikipedia
`1 per 4,000 per Wikipedia
`Lin 733 per Wikipedia
`1in 4,000 per Wikipedia
`Lin 3,100 ta 4,600 per OMIM
`53 of Europeans are het, per Wikipedia
`Lin 10,000 to 15,000 per Wikipedia
`Aboout 5% of Alzheimer cases
`
`Lin 3,600 males; 1 in 4,000 - 6,000 females, per Wikip
`Lin 40,000 but much higher in Ashkenazi Jews, per Wi
`Lin 5,000 - 10,000 per Wikipedia
`2in 1,000 per Wikipedia
`5-10 per 100,000 per Wikipedia
`0.2-0.5% per Wikipedia
`1in 5,000 per About.com
`Lin 3,000 to 5,000 per Wikipedia
`1.5-8% per Wikipedia
`1 per 15,000 per Wikipedia
`1 per 60,000 per Wikipedia
`1 per 4,756 per a PubMedarticle
`1in 5,000 in USA, 1 in 500 Atrican Americans
`Lin 8,000 to 10,000 per on-line article.
`2-3% in Ashkenazi Jews, Irish, Cajun; 0.3% otherwise
`Complicated - TED
`
`Personalis EX2115.2
`
`
`
`GENETIC DISEASES WHICH MAY BE CHALLENGING FOR NEXT-GEN SEQUENCING DIAGNOSIS
`
`DISEASES|WPE OF CHALLENGE
`
`Mutations of FBN-1 gene: 15-30% are de novo
`
`CNV ofall or part of Chr 21
`Duplication of a large region in Chr 17p22, including the PMP2?2 gene
`PRIM2 susceptibility gene is in a compression
`Het or homozygous deletion of RHD gene
`HBB gene has multiple pseudogenes
`GBA gene has at least one nearby pseudogene
`CYP450 family has many (58?) pseudogenes(e.g. CYP3A5P1 for CYP3A5)
`Tri-nucleotide repeat (normally 6-55 becomes 230-4000) in FMR1
`Variable tri-nucleotide repeat in the HTT gene, on Chr 4 (28 - >60)
`GAA gene is about 80% GC
`
`Down's syndrome
`Charcot-Marie-Tooth Disease
`Breast cancer
`Rh factor (ABO blood grouping)
`Beta Thalassemia
`Gaucher Disease
`Drug metabolism
`Fragile X syndrome
`Huntington's
`PompeDisease
`Marfan Syndrome
`
`CNV
`CNV
`CNV
`CNV
`Pseudogenes
`Pseudogenes
`Pseudogenes
`Tri-nucleotide repeat
`Tri-nucleotide repeat
`High GC content
`Hign de novo rate
`
`Personalis EX2115.3
`
`
`
`Coverage Graph
`Shows Medically
`Relevant Large Het
`Deletion
`
`Heterozygous deletion of
`approx. 70kbp on Chr 1
`completely eliminates one
`copy of the RHD gene.
`This deletion, heterozygous in
`40% of Europeans, and
`homozygous in 16%, is
`responsible for Rh-negative
`ABO blood typing when
`homozygous.
`
`Personalis EX2115.4
`
`
`
`Large Het or Hom Deletions Can Be Seen From Coverage
`Example: 40kbp Het / Hom Del in Chr 2
`West family genome data, Chr2 34-35M base range
`
`Father
`
`Daughter
`
`Mother
`
`Son
`
`Personalis EX2115.5
`
`
`
`Smaller Heterozygous Deletions Can Also Be Detected By Read-Pairs With
`Anomalous Apparent Spacing
`(This particular example is inside a compression, so het SNP’s are observed inside a het deletion)
`
`Personalis EX2115.6
`
`
`
`Coverage Distribution Over All of Chromosome 5
`Drop-Outs Due to Centromere and (Red line) Segmental Duplication
`Zoomed-In on Next Slide
`
`Personalis EX2115.7
`
`
`
`1.85 Mbp Coverage Drop-Out on Chr 5 Due To Segmental Duplication
`
`Personalis EX2115.8
`
`
`
`Coverage Over All of Chromosome 21 – Potential to Detect Down’s Syndrome
`Trisomy over part of the chromosome should be clear from this graph.
`Trisomy over all of the chromosome should be clear from chromosome coverage ratios
`
`Personalis EX2115.9
`
`
`
`AG or GA het SNP loci from Chromosome 1 of Anne’s genome sequence, at which exactly 30 reads were used
`to make the call. This shows that the allelic balance matches the expected binomial probability distribution
`quite closely.
`
`Personalis EX2115.10
`
`
`
`
`DNASequencing
`
`
`
`
`
`Coverage:Fourfamilymemberscombined
`
`normalcoveragea singleperson
`
`Regionofof3x AA as whass maaam @—|LOC tri-allelicina
`YY
`normaleonof
`
`
`crownof1xnormalcrown
`
`
`At
`
`
`Tri-Allelic Loci Cluster in Region of 3x normal Sequencing Coverage
`Coverage : Four West Family Members Total, Chr 6 : 57 - 58M
`
`600
`
`500
`
`Region of 2x
`
`400
`
`100
`
`57,000,000
`
`57,200,000
`
`57,400,000
`
`57,600,000
`
`57,800,000
`
`58,000,000
`
`Position Along Chromosome 6 (bases)
`
`Personalis EX2115.11
`
`
`
`The region which appears to have 3x nominal overall coverage also shows an allelic distribution which clearly
`confirms the 3-fold repeat structure.
`
`Personalis EX2115.12
`
`
`
`Paired-End Read Length Distribution
`A Simple Sample Prep QC Metric
`
`Personalis EX2115.13
`
`
`
`Distribution of Raw-Read Individual Base Q-Scores Along A Read
`A Simple Sequencing QC Metric
`
`Personalis EX2115.14
`
`
`
`Coverage Histogram vs Poisson
`A Simple Sequencing QC Metric
`In this example, 13% of SNP Genotypes Were Based on < 10-fold Coverage
`
`Personalis EX2115.15
`
`
`
`Coverage Is Significantly Correlated Between Individuals
`
`Personalis EX2115.16
`
`
`
`Comparison of coverage dips / gaps in the same region of
`
`John
`
`two genetically unrelated people
`Judy
`
`Personalis EX2115.17
`
`
`
`Coverage Variation Correlated With Alu Repeats
`Illumina Alignment From Early 2010
`
`Personalis EX2115.18
`
`
`
`Initial results with the new Illumina
`V2e Alignment Software
`
`Based on a West Family Genome Aligned Using V2e
`
`John & Anne West
`Oct 12, 2010
`
`Personalis EX2115.19
`
`
`
`Comparison of coverage histograms in a “typical” region of 250,000 bases
`starting at position 57,000,000 on Chromosome 6.
`
`Personalis EX2115.20
`
`
`
`Coverage becomes much closer
`to Poisson with the Illumina
`Eland v2e algorithm, particularly
`in short repeats (SINE
`elements) e.g. Alu repeats.
`
`Personalis EX2115.21
`
`
`
`Most of the coverage increase is in regions where the original alignment
`yielded low coverage. Loci which had 10-fold coverage in the original
`alignment, for example, averaged about 25-fold coverage in the V2e alignment.
`
`Personalis EX2115.22
`
`
`
`Example comparing DNA sequencing coverage from the original
`alignment of one of our genomes with the same region after use of
`the new V2e alignment software.
`
`Personalis EX2115.23
`
`
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