SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then...
Transcript of SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then...
![Page 1: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/1.jpg)
SNP allele analysis: UPD and
then some
Hutton M. Kearney, PhD , FACMG
![Page 2: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/2.jpg)
Copy number + SNP microarrays
AGILENT AFFYMETRIX
OGT ILLUMINA
![Page 3: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/3.jpg)
Affymetrix experience
• SNP 6.0 clinical use from 2008-2011
• CytoScan HD alpha testing site Spring, 2011
– Product evaluation, protocol and performance feedback provided
– “Proof of principle” exchanges with more than 100 laboratories
• CytoScan clinical service launch July, 2011
• Over 2,000 samples run on this platform
• Tissues types validated:
– peripheral blood
– buccal
– villi/POC, amniotic fluid, skin
– also by proxy: tumors, bone marrow, leukemic bloods
![Page 4: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/4.jpg)
Allele detection (Affy simplified)
A
B
Probe designed specific to “A” genotype
Probe designed specific to “B” genotype
A
B
A
B
A
B
AA genotype BB genotype AB genotype
0.5 + 0.5
0.5 + 0.5
0.5
0.5
![Page 5: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/5.jpg)
SNP allele calls
Each point represents a single SNP interrogated by “A” + “B” allele probes
Arbitrary fluorescence unit of haploid locus (single allele) = 0.5 Genotype “AA” = [0.5+0.5] – [0] = 1
Genotype “AB” = [0.5] – [0.5] = 0
Genotype “BB” = [0] – [0.5+0.5] = -1
AA
BB AB
We don’t typically genotype these samples, but instead derive general information regarding allele state
[A]-[B]=?
1 0
-1
![Page 6: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/6.jpg)
Allele difference pattern supportive of deletion CNV
Deletions
A
B
![Page 7: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/7.jpg)
Allele difference pattern supportive of duplication CNV
AAA
BBB
AAB
ABB
![Page 8: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/8.jpg)
Allele difference pattern in large region of homozygosity
![Page 9: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/9.jpg)
Which is it, LOH, AOH, ROH, LCSH?
• LOH: loss of heterozygosity – This term describes an event where heterozygosity (once
present) is now absent – Copy number neutral or deletion
• AOH: absence of heterozygosity – This term describes an observation where no heterozygosity is
present – Copy number neutral or deletion
• ROH: runs of homozygosity – This term is specific to copy number neutral homozygosity – Does not apply to hemizygous deletions
• LCSH: long contiguous stretch of homozygosity – This term is interchangeable with ROH
![Page 10: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/10.jpg)
Homozygosity-significant? • Consanguinity/ Isolated ethnic population
– Relevant only to narrow focus on single-gene (recessive) disorders
– Rarely (or not so rarely…), uncovers cases of abuse/incest as an incidental finding
• Uniparental disomy – Inheritance of both homologues from the same parent
• Trisomy rescue, mitotic recombination (segmental)
– Implications for homozyosity, undetected mosaicism, as well as abnormal phenotypes due to differential methylation in maternal/paternal germline
![Page 11: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/11.jpg)
Clinical utility of homozygosity detection
References:
Kearney, HM, Kearney, JB, and Conlin, LK. Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy and recessive single-gene mutations. Clinics in Laboratory Medicine 31(4):595-613, 2011
Papenhausen P, et al. UPD detection using homozygosity profiling with a SNP genotyping microarray. Am J Med Genet 155A:757-68, 2011
• Approximately 3% of our clinical cases have excessive homozygosity – <1% of our cases represent uniparental disomy
– Most LCSH is consanguinity (occasionally abuse suspected)
– ~10% of these cases (UPD or consanguinity) have successful autozygosity mapping to confirm homozygous mutation responsible for recessive disease.
![Page 12: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/12.jpg)
Homozygosity reporting criteria
• LCSH is filtered at ≥3 Mb to unclutter the analysis
– Most individuals have numerous LCSH < 3 Mb totaling up to 2-5% of genome
• Any LCSH greater than 3-15 Mb is scrutinized
– Common/recurrent LCSH disregarded (maintain BED file) – Single chromosome involved?
• Consider UPD and associated mechanisms • Many (or most!) are not associated with UPD
– Throughout genome? • We report cases with > 2% autosomal LCSH (>3 Mb)
– Consider autozygosity mapping for recessive conditions in all cases
![Page 13: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/13.jpg)
Isolated LCSH leading to UPD detection
![Page 14: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/14.jpg)
UPD: Trisomy rescue mechanism
Gametes
Somatic Tissue
Zygote
disomy trisomy
Normal Trisomy “rescue”
UPD
OR
Non-disjunction to restore disomy
Meitoic recombination will generate regions of iso- and heterodisomy
![Page 15: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/15.jpg)
Meiosis I nondisjunction (heterozygous at centromere)
Figure: Kearney et al (2011) Clinics in Laboratory Medicine 31(4):595-613
M I
M II
![Page 16: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/16.jpg)
Meiosis II nondisjunction (homozygous at centromere)
Figure: Kearney et al (2011) Clinics in Laboratory Medicine 31(4):595-613
M I
M II
![Page 17: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/17.jpg)
UPD: Trisomy/monosomy rescue
Figure: Kearney et al (2011) Clinics in Laboratory Medicine 31(4):595-613
![Page 18: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/18.jpg)
Not all UPD events generate LCSH
![Page 19: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/19.jpg)
Heterodisomic vs Isodisomic UPD
Heterodisomic segments are still UNIPARENTALLY derived (and methylated as such)…the placement of LCSH relative to imprinting loci is irrelevant when whole-chromosome UPD is involved.
![Page 20: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/20.jpg)
A sampling of UPD15 and associated LCSH patterns (courtesy of Sarah South/ARUP)
15 Mb
6 Mb
19 Mb
All three cases were confirmed UPD 15 by methylation – Prader Willi
![Page 21: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/21.jpg)
More UPD15 (Proof of principle study courtesy of Stuart Scott/ Mount Sinai)
Homozygosity around the centromere suggests MII error
![Page 22: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/22.jpg)
UPD15 (trio analysis and mechanism)
mother
proband
LCSH block seen in mother (also in common LCSH track maintained by lab)
![Page 23: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/23.jpg)
Tracking AOH experience
AOH block seen in >5% of all cases
![Page 24: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/24.jpg)
Trio analysis (heteroUPD segment)
HeteroUPD: One parent will have
apparent violations of paternity; all
alleles will agree with UPD parent (both parental
alleles inherited)
![Page 25: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/25.jpg)
Trio analysis (isoUPD segment)
IsoUPD: One parent will have
apparent violations of paternity: all
proband’s alleles will be homozygous
and dervied from UPD parent
![Page 26: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/26.jpg)
Small regions of LCSH associated with UPD (Proof of principle study courtesy of Erik Thorland/Mayo Clinic)
~5 Mb terminal homozygosity on chromosome 15; confirmed PraderWilli syndrome
![Page 27: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/27.jpg)
Segmental UPD
When UPD is created through somatic structural events (mitotic crossover, break-induced replication), it DOES matter whether the region of homozygosity maps to imprinted loci. e.g.: segmental UPD 11p (usually mosaic) is common in Beckwith Wiedemann syndrome.
Figure: Kearney et al (2011) Clinics in Laboratory Medicine 31(4):595-613
![Page 28: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/28.jpg)
Single segment LCSH; consanguinity?
26 Mb LOH stretch on chr 10 Parents very distantly related (3rd cousins once removed)
27 Mb LOH stretch on chr 17 Parents very distantly related (2rd cousins once removed)
Carriers of balanced rearrangements that suppress recombination ???
11 meiotic exchange opportunities
9 meiotic exchange opportunities
![Page 29: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/29.jpg)
Genome-wide LCSH seen in consanguinity
Figure: Kearney et al (2011) Clinics in Laboratory Medicine 31(4):595-613
![Page 30: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/30.jpg)
% Autosomal LCSH
751,053 ÷ 2,881,033 = ~26% autosomal LCSH (>3 Mb)
![Page 31: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/31.jpg)
% Autosomal LCSH
![Page 32: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/32.jpg)
Relationship Degree of Relationship
Coefficient of Inbreeding for offspring
% Expected homozygosity
Full siblings First 0.25 25%
Parent/child First 0.25 25%
Half siblings Second 0.125 12.5%
Uncle/niece or Aunt/nephew
Second 0.125 12.5%
Double first cousins Second 0.125 12.5%
Grandparent/ grandchild Second 0.125 12.5%
First cousins Third 0.0625 6%
First cousins once removed
Fourth 0.03125 3%
Second cousins Fifth 0.015625 1.5%
(assuming outbred population…)
![Page 33: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/33.jpg)
Chromosome ~start ~stop ~ size (Mb)
1 52 76.5 24.5
2 0.6 11.2 10.6
2 169.5 175.3 5.8
2 220.3 238.7 18.4
3 67.7 77.8 10.1
5 135.5 146 10.5
5 159 173.5 14.5
6 12.3 20.7 8.4
8 26.3 53.5 27.2
8 128 146.2 18.2
10 62 82.3 20.3
12 5.2 10.2 5
12 52.8 60.7 7.9
15 18.5 30.7 12.2
15 55.4 72.6 17.2
TOTAL: 210.8
1-22 TOTAL 2,868
% LCSH
(conservative
estimate)
7.4%
Estimation of degree of parental relationship
Presumed first cousins, confirmed by family history
1/2
1/8
1/16=6.25%
Our method: ∑ autosomal LCSH >3Mb in size/total autosomal length
![Page 34: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/34.jpg)
Previous language for consanguinity cases >2% IBD
“…Notably, numerous independent regions of
apparent homozygosity were detected in this
specimen, encompassing greater than 18% of
this individual's genome. This result is not
diagnostic of, but raises the suspicion for the
possibility of a recessive single gene disorder…”
![Page 35: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/35.jpg)
American College of Medical Genetics and Genomics standards and guidelines for reporting suspected
consanguinity as an incidental finding of genomic testing
Genetics in Medicine (in press) C. Rehder, K. David, B. Hirsch, H. Toriello, C. Wilson, and H. Kearney
“The guidelines presented here are designed to assist clinical laboratories in the management and reporting of microarray and exome/genome sequencing findings that suggest parental consanguinity, with a primary focus on detection and reporting language.”
![Page 36: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/36.jpg)
ACMG recommended reporting for consanguinity >10%
“Several large regions of homozygosity (_ Mb or larger) were detected, encompassing >_% of the genome. Although this result is not diagnostic of a specific condition, it raises the possibility of a recessive disorder with a causative gene located within one of these regions. Additionally, these results could indicate a familial relationship (first or second degree) between this individual’s parents. A genetics consultation is recommended.”
![Page 37: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/37.jpg)
Case of consanguinity for discussion
• Newborn born to a 15 yo
• Child diagnosed with pseudohypoaldosteronism – Defect in sodium transport with
salt wasting, FTT, cardiac arrythmia (with hyperkalemia)
• Rare recessive seen in mainly consanguineous families
• CMA revealed 32% genomic homozygosity, SCNN1A gene included
• Molecular testing for SCNN1A revealed homozygous mutation, predicted deleterious
SCNN1A: chr12:6,326,272-6,356,784
![Page 38: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/38.jpg)
Ethical considerations
• Results discussed with mother, she disclosed the FOB was her paternal half brother (reportedly consensual, also a minor)
– Half brother would expect to yield 12.5% LOH…32% LOH seen in this child
– How certain is this prediction for 1st degree?
• Case was discussed with legal team at Mission, and no further follow up was recommended.
![Page 39: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/39.jpg)
A second case for discussion…
• 17yo with cleft lip, juvenile arthritis, hypermobility
• CMA revealed >18% homozygosity
– 1st degree (25%) vs. 2nd degree (12.5%)
• Very unusual situation:
– mother was adopted with no family history available
– father was raised in foster care, but he reports large and detailed biological family history
![Page 40: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/40.jpg)
Ethical considerations
• Possible siblings/ half-sibs?
• Happily married with no knowledge of relationship
• No future children (mom with hysterectomy)
• Not diagnostic of any specific condition
• Family was not informed of homozygosity
![Page 41: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/41.jpg)
Considerations for consanguinity detection
• Serious ELSI implications
• Homozyosity measurement is an indirect measure of consangunity and does not substitute for a paternity test
– Caution when implying degree of relationship!!
• Parents should be counseled clearly BEFORE test is administered, preferably with formal consent form upfront
![Page 42: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/42.jpg)
Identification of homozygous mutations in cases with excessive LCSH
(IBD or UPD)
![Page 43: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/43.jpg)
Pop quiz
Is it helpful to include consider regions of homozygosity on the X in a female
when performing autozygosity mapping???
![Page 44: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/44.jpg)
Autozygosity mapping: Case 1
• 35 yo female
• Retinitis pigmentosa
• Hearing loss
• Suspected Usher syndrome type unknown (9+ targets)
• CMA revealed no copy number imbalances, but several large stretches of LSCH seen (below reporting criteria of 2%)
• LCSH regions checked for Usher-related genes
![Page 45: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/45.jpg)
USH2A homozygous mutation within region of LCSH
![Page 46: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/46.jpg)
Using .bed files to aid in autozygosity mapping-Joubert syndrome example
![Page 47: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/47.jpg)
Autozygosity mapping: Case 2
• 22 yo male referred for dev delay
• 10% of genome homozygous
• Follow-up with family revealed hx of abuse
(uncle-niece)
– Predicted level at 12.5%
![Page 48: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/48.jpg)
• Several cells showed abnormalities involving the pericentromeric region of chr 1
• These abnormalities are hallmarks of ICF syndrome – Immunodeficiency-Centromeric
Instability-Facial Anomalies Syndrome
– less than 30 cases reported world-wide
• Follow-up with physician revealed that patient suffered lifetime of immunodeficiency
Radial formation
Isochromosome 1p
Information from chromosome screen pointed a new finger…
![Page 49: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/49.jpg)
DNMT3B in region of homozygosity
DNMT3B
![Page 50: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/50.jpg)
• G587: Highly conserved residue (human, mouse, zebrafish) – Located in catalytic domain (methyltransferase)
• Predicted deleterious mutation in protein prediction models for G587D substitution
DNMT3B ICF mutation spectrum
Modified from: http://bioinf.uta.fi/DNMT3Bbase
G587D
patient
control
DNMT3B sequencing revealed a novel homozygous mutation
![Page 51: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/51.jpg)
www.ccs.miami.edu/cgi-bin/ROH/ROH_analysis_tool.cgi
Genet Med advance online publication 25 October 2012
![Page 52: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/52.jpg)
![Page 53: SNP allele analysis: UPD and then some - Millennium Science · SNP allele analysis: UPD and then some Hutton M. Kearney, PhD , FACMG](https://reader031.fdocuments.us/reader031/viewer/2022022012/5b1652fd7f8b9a6d6d8b463d/html5/thumbnails/53.jpg)
Acknowledgements
Fullerton Genetics Center
• Joseph B. Kearney, PhD
• Microarray technologists:
– Pablo Sagaribay
– Renee Casey
– Connie Monroe
– Melissa Shook
• Bill Allen, MD
• Ellen Boyd, MD
• Fullerton genetic counselors
Fullerton array team
Colleagues (data presented)
• Laura Conlin, PhD (CHOP)
• Stuart Scott, PhD (Mt. Sinai)
• Sarah South, PhD (ARUP)
• Erik Thorland, PhD (Mayo)
Affymetrix
• Richard Shippy