What lies beneath: challenges in reporting SNP array results Jonathan Waters Challenges in variant interpretation Austin Court, Birmingham Monday 4 th July 2016
What lies beneath: challenges in reporting SNP array results Why talk about SNP array reporting now? What are SNP arrays? Experience from GOSH and other centres Pointers for Best Practice Guidelines for array and beyond
What lies beneath: challenges in reporting SNP array results Why talk about SNP array reporting now? number of laboratories considering using constitutional SNP arrays what are we obliged to disclose and report? consanguinity : safeguarding / disclosure legal framework beyond the scope of this presentation - email traffic around the above best practice guidelines imminent What are SNP arrays? Experience from GOSH (and other centres) Pointers for Best practice guidelines for array reporting
What lies beneath: challenges in reporting SNP array results Why talk about SNP array reporting now? What are SNP arrays? Experience from GOSH and other centres Pointers for Best Practice Guidelines for array and beyond
SNP (single nucleotide polymorphism) array Affymetrix 750K - a copy number track (above) - a SNP track which counts the relative allele peak ratio of 250K biallelic loci (below) Copy number track 14 15 16 SNP (allele peak ratio) track aa ab bb Chromosome 15 is copy number neutral but shows LCSH (Long Continuous Stretches of Homozygosity) across the whole chromosome SNP pattern for chromosome 15 is either aa or bb but not ab 13G13897: 12 yr old / moderated LD / statemented learning at pre-school level / H/O global delay Angelman syndrome (MLPA-MS confirmed)
What are SNP arrays? - a slide on nomenclature AoH Absence of Heterozygosity (or Autozygosity) RoH Region of Homozygosity LCSH (Long Continuous Stretches of Homozygosity) - copy number neutral - size called is software determined (InfoQuant: >=10Mb) LOH Loss of Heterozygosity - implies an acquired change from a germ line in a proportion of daughter cells Haem/Onc
Experience from GOSH Absence of Heterozygosity (AoH) What are SNP arrays? Why talk about SNP arrays now? Experience from GOSH AoH: array findings: what we report AoH: what we see (and how often) Best practice guidelines and beyond
What SNP array findings do we report? Copy number information - pathogenic findings - including NSCLs (neurocognitive susceptibility loci) - VOUS : clinically actionable i.e. (usually) where we want to perform segregation analysis (by requesting parental follow-up) - CNVs polymorphic variants of no known clinical significance we do not routinely report CNVs SNP (Single Nucleotide Polymorphism) information. - Absence of Heterozygosity (AoH):we do not routinely report AoH findings
SNP array results: generated lists: CNV (triage) + LOH (AoH)
Can we categorise AoH ( LOH ) results and what do they look like? Isolated lengths of Absence of Heterozygosity (AoH) isolated ancestral block of AoH single chromosome iso-uniparental UPD : whole or segmental inspection of regions or loci for AoH on the basis of a clinical suspicion of a manifesting recessive disorder associated with a limited number of recessive loci Multiple lengths of Absence of Heterozygosity (AoH) Referral reasons can include: consanguinity or consanguineous parents or parents are first cousins
What do the AoH ( LOH ) results look like? : isolated findings Isolated lengths of Absence of Heterozygosity (AoH) isolated ancestral block(s) of AoH single chromosome iso-uniparental UPD : whole or segmental inspection of particular regions or loci for AoH on the basis of a clinical suspicion of a manifesting recessive disorder associated with a particular or a limited number of recessive loci
Reporting policy for: isolated length(s) of Absence of Heterozygosity (AoH) Isolated lengths of Absence of Heterozygosity (AoH) isolated ancestral block(s) of AoH single chromosome iso-uniparental disomy : whole or partial inspection of particular regions or loci for AoH on the basis of a clinical suspicion of a manifesting recessive disorder associated with a limited number of recessive loci Multiple lengths of Absence of Heterozygosity (AoH) referral: consanguinity or consanguineous parents or parents are first cousins clinical request for inspection of AoH regions on basis of a clinical suspicion of an inappropriate sexual relationship between the parents of a child (incest)
Isolated lengths of Absence of Heterozygosity (AoH) isolated ancestral block(s) of AoH single chromosome iso-uniparental UPD : whole or segmental inspection of particular regions or loci for AoH on the basis of a clinical suspicion of a manifesting recessive disorder associated with a limited number of recessive loci Multiple lengths of Absence of Heterozygosity (AoH) referral: consanguinity or consanguineous parents or parents are first cousins
16G10667 parents are first cousins (case A) AOH distribution
Multiple lengths of Absence of Heterozygosity (AoH) Consanguinity Referral reasons include: consanguinity or consanguineous parents or parents are first cousins Consanguineous unions defined as: marriages or relationships between second cousins and closer (Broman KW et al., 1999; Woods CG at al., 2006) - recent studies (of AoH) in different human populations reveal that they are very common and longer (>1Mb) than expected (Kirin M et al., 2010) - close consanguineous unions (mostly first cousin marriages) are common in some populations (Sund KL et al, 2012): up to 60% in some populations 0.1-1.5% in North America - associated with an increased risk of manifestation of autosomal recessive disorders
Snapshot audit one month s postnatal reports (n=252) (March 2016): No of AoH (>=10Mb) (autosomes only) Cases No AoH 1 to 4 AoH 5 to 9 AoH 10 to 14 AoH 15-19 AoH 20-24 AoH
Snapshot audit one month s postnatal reports (March 2016): No of AoH (>=10Mb) autosomes only (n=252) n o. o f c a s e s 10 9 8 7 6 5 4 3 2 1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 no of calls per case (>=10Mb) 24 cases with no calls (n=221) not shown
16G10667 parents are first cousins (case A) AOH distribution sum of >=10Mb AoH calls = 210.7/2881Mb (7.3%)
16G03680 (case B) clinical interest in degree of relatedness sum of >=10Mb AoH calls = 765.1/2881Mb (25.5%)
Snapshot audit one month s postnatal reports (March 2016): No of AoH (>=10Mb) autosomes only (n=252) n o. o f c a s e s 10 9 8 7 6 5 4 3 2 1 0 GOSH case: first cousin union: manifested with just a single large (>10Mb) segmental UPD and no other called AoH (>=10Mb) Case A: parents first cousins Case B clinical interest 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 182419 no of calls per case (>=10Mb) cases with no calls (n=221) not shown
Can we quantify? Case B Case A from: Lipscomb Sund K. et al. Genetics in Medicine 2013, 15,70-78
Reporting policy for: multiple length(s) of Absence of Heterozygosity (AoH) Multiple lengths of Absence of Heterozygosity (AoH) referral: consanguinity or consanguineous parents or parents are first cousins clinical request for inspection of AoH regions because of the possibility of a consanguineous relationship - very rare: n=2 in three years (>9000 postnatal referrals)
Reporting strategy for: multiple lengths of Absence of Heterozygosity (AoH) Multiple lengths of Absence of Heterozygosity (AoH) clinical request for inspection of AoH regions Case B Case B report Multiple long contiguous stretches of homozygosity (LCSH) were identified by Affymetrix 750K SNP microarray these are usually indicative of regions which are identical by descent (IBD) and usually reflect a shared genetic heritage for the patient's parents LCSH (AoH) is not a genetic abnormality but is associated with an increased risk of the manifestation of recessive genetic disorders
What lies beneath: challenges in reporting SNP array results Why talk about SNP array reporting now? What are SNP arrays? Experience from GOSH and other centres Pointers for Best Practice Guidelines for array and beyond
Pointers for Best Practice Guidelines for SNP arrays and beyond AoH is commoner in the general population that was previously thought Consanguinity is now relatively common in some UK populations reporting justifiable where there is a specific clinical request requests are very rare (in our expereience) (n=2 in three years) wording as per example in this talk (Case B) conservative approach do no harm virtual MDT approach helpful (cf prenatal array reporting) Quantitation of consanguinity (as judged by % autosomal AoH) fraught with difficulty: under-estimation and failure to take into account prior F/H: e.g. double first cousin marriages American (ACMG&G) guidelines are worth noting (Rehder CW et al., Genet in Medicine, 2013) new version in preparation American reporting practice based on lab questionnaire very variable approach (Grote L et al., Genet in Medicine 2012) and finally: beyond SNP arrays for the detection of AoH
and finally: beyond SNP arrays for the detection of AoH Ultimately our aim, using the best available technology, is to detect candidate manifesting autosomal recessive loci that may be causative of a particular phenotype Candidate manifesting autosomal recessive loci will be more prevalent in individuals who are the product of a consanguineous unions but NGS technologies will allow us to focus on the genes themselves to provide or aid in a genetic diagnosis Acknowledgements: colleagues (both scientific and clinical) at RGS, GOSH - particularly Debs Morrogh Eddie Maher (Edinburgh), Dom McMullan (Birmingham), Una Maye (Liverpool), Ingrid Simonic (Cambridge)