BioCuration WG Variant Curation - PowerPoint Presentation

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BioCuration WGVariant Curation

Steven Harrison

June 8 2017

sharrison@bwh.harvard.edu

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Slide3

RASopathies

Developmental

Delay

Cardiovascular

Metabolism

Hereditary Cancer

Sequence Variant Interpretation

WG

Harmonize recommendations for modifying ACMG guidelines

Gene/Disease Specific ACMG Guidelines

General recommendations to ACMG Guidelines

ClinGen Disease

WGs

ACMG/AMP Guidelines

Slide4

“…To provide critical flexibility to variant classification, some criteria listed as one weight can be moved to another weight using professional judgment, depending on the evidence collected…”

No direction was provided regarding what criteria code to use in these instances

Slide5

To document strength-modified evidence, SVI recommends using the original criteria code followed by an underscore and new level of strength

Pathogenic

Supporting

Moderate

Strong

Segregation

Data

Co-segregation with disease in multiple affected family

members

PP1

Increased segregation data

Slide6

To document strength-modified evidence, SVI recommends

using the original criteria code followed by an underscore and new level of strength

Pathogenic

Supporting

Moderate

Strong

Segregation

Data

Co-segregation with disease in multiple affected family

members

PP1

# Co-segregation with disease in multiple affected family

members

PP1_Moderate

## Co-segregation with disease in multiple affected family

members

PP1_Strong

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Population

Data

Segregation

Data

Prevalence in affecteds statistically increased over

controls (OR approach)

Variant identified in

###

probands with consistent phenotypes

PS4

MAF is too high for disorder BA1/BS1

Observation in controls inconsistent with disease

penetrance BS2

Predicted null variant in a gene where LOF is a known mechanism of

diseasePVS1

De novo (paternity & maternity confirmed)

PS2

Well-established functional studies show a deleterious effect PS3

Novel missense change at an AA residue where a different pathogenic missense change has been seen

before PM5

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

De novo

(without paternity & maternity confirmed

)

PM6

Non-segregation with

disease

BS4

Patient’s

phenotype

or FH highly specific for gene

PP4

For

AR

disorders, detected in

trans

with a

path variant

PM3

Found in case with an alternate

cause

BP5

Multiple lines of

comp

evidence

suggest

no impact

BP4Missense when only truncating cause disease BP1Silent variant w/ non predicted splice impact BP7In-frame indels in repeat w/out known function BP3

Well-established functional studies show no deleterious effect BS3

Mutational hot spot or well-studied functional domain PM1

Same AA change as an established path variant PS1

Protein length changing variant PM4

Observed in trans with a dominant variant or Observed in cis with a pathogenic variant BP2

Functional Data

# Co-seg w/ disease in multiple affected family members PP1

De novo Data

Allelic Data

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Missense in gene with low rate of benign missense

variants and path. missenses common PP2

Other Data

Benign

Pathogenic

## Co-

seg w/ disease in multiple affected family members PP1_Moderate

### Co-seg w/ disease in multiple affected family members PP1_Strong

# De novo (without paternity & maternity confirmed) PM6_Strong

# For AR disorders, detected in trans with a path variant PM3_Strong

# Found in case with an alternate cause BP5_Strong

Functional

studies show a deleterious effect

PS3_Moderate

Variant identified in

##

probands with consistent phenotypes

PS4_Moderate

Variant identified in

#

probands with consistent phenotypes

PS4_Supporting

Slide8

MAF is too high for disorder

BA1/BS1

Observation in controls inconsistent with disease penetrance

BS2

Absent in population databases

PM2

Prevalence in

affecteds

statistically increased over controls

PS4

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

POPULATION DATA (BA1, BS1, BS2, PM2, PS4

)

Slide9

MAF is too high for disorder

BA1/BS1

Observation in controls inconsistent with disease penetrance

BS2

Absent in population databases

PM2

Prevalence in

affecteds

statistically increased over controls

PS4

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

POPULATION DATA (BA1, BS1, BS2, PM2, PS4

)

Slide10

Proposed BA1: Allele frequency is >5% in any general continental population dataset of at least 2,000 alleles for a gene without a gene- or variant-specific recommendation

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Proposed BA1: Allele frequency is >5% in any general continental population dataset of at least 2,000 alleles

for a gene without a gene- or variant-specific recommendation

Can compare to individual, continental populations (>2,000 alleles)

Tested individual does not need to match ethnic origin of population dataset used

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Proposed BA1: Allele frequency is >5% in any general continental population dataset of at least 2,000 alleles for a gene without a gene- or variant-specific recommendation

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Proposed BA1: Allele frequency is >5% in any general continental population dataset of at least 2,000 alleles for a gene without a gene- or variant-specific recommendation

Gene

Variant

Max MAF

GJB2

NM_004004.5: c.109G>A (V37I)

0.072

EAS-ExAC

HFE

NM_000410.3: c.845G>A (C282Y)

0.051

NFE-ExAC

BTD

NM_000060.4:

c.1330G>C (D444H)0.054 FIN-

ExAC

Clinical domain working groups can define BA1 thresholds <5% (based on prevalence and penetrance)

Exception list for non-benign alleles >5% in continental populations

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Determine Max Credible Population AFPrevalence X

Heterogeneity

Penetrance

BA1

(stand alone criteria for Benign)

Use MOST conservative estimates

BS1

(Benign strong criteria)

Use less conservative estimates

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Determine Max Credible Population AF

BA1 Max Credible AF: 0.00487 (~0.5%)

Assuming…

1/40,000 prevalence

95% of Pompe due to

GAA

All of

GAA

-Pompe caused by single variant

Penetrance 100%

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Determine Max Credible Population AF

BS1 Max Credible AF: 0.00096 (~0.1%)

Assuming…

1/300,000 prevalence

95% of Pompe due to

GAA

One

GAA

variant account for 50%

Penetrance 85%

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Great tool to help determine AF thresholds:https://cardiodb.org/allelefrequencyapp/

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Filtering Allele Freq = highest AF that would be compatible with the observed allele count (95% CI Poisson)

Slide19

PM2 – “Absent”Dominant versus

Recessive

However, dominant does

not

need to be 100% absent, depending on penetrance / age of onset

Hypertrophic cardiomyopathy: <0.00004 (~5 alleles max)

RASopathy: strictly absent

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PM2 – “Absent”PM2 threshold could be

inverse of BS1

BA1: ≥0.1%

BS1: ≥0.05%

PM2: <0.05%

IF disorder is recessive or reduced penetrant dominant

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MAF is too high for disorder

BA1/BS1

Observation in controls inconsistent with disease penetrance

BS2

Absent in population databases

PM2

Prevalence in

affecteds

statistically increased over controls

PS4

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

POPULATION DATA (BA1, BS1, BS2, PM2, PS4

)

Generally, should not be used based on occurrences in ExAC/

gnomAD

as phenotypes are unknown

If disorder IS NOT penetrant at early age, consider removing this criteria

Can also add occurrence thresholds

RASopathy:

variant identified in ≥3 well

phenotyped

individuals

Slide22

MAF is too high for disorder

BA1/BS1

Observation in controls inconsistent with disease penetrance

BS2

Absent in population databases

PM2

Prevalence in

affecteds

statistically increased over controls

PS4

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

POPULATION DATA (BA1, BS1, BS2, PM2, PS4

)

Because the denominator for cases/probands is not always known (and thus cannot calculate an OR), guidelines state PS4 can also be used to count probands w/ consistent phenotypes

Slide23

MAF is too high for disorder

BA1/BS1

Observation in controls inconsistent with disease penetrance

BS2

Variant identified in

#

probands with consistent phenotypes

PS4_Supporting

Absent in population databases

PM2

Variant identified in

##

probands with consistent phenotypes PS4_Moderate

Prevalence in

affecteds statistically increased over controls (OR method)

Variant identified in #

## probands with consistent phenotypes PS4

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

POPULATION DATA (BA1, BS1, BS2, PM2, PS4

)

PS4 could be used for typical case-control studies with an OR

OR

PS4 could be used for multiple unrelated probands with consistent phenotypes

Slide24

Comparison of PS4 Specification

PS4_Supporting

PS4_Moderate

PS4 (Strong)

PM2 threshold

MYH7

≥2 probands

≥6 probands

≥15 probands

<0.004%

RASopathy

≥1 probands

≥3 probands

≥5 probands

Strictly absent

Slide25

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Novel missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

Slide26

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Novel missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

BP1 could also be used for:

LOF variants in a gene where the disease:

is caused by

GOF

variants

i

s caused by dominant/negative LOF variants

Slide27

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Novel missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

Slide28

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

Slide29

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

General modifications for PM5 and PS1:

Allow criteria to be used for analogous genes

[HRAS, NRAS, KRAS] ; [MAP2K1, MAP2K2] ; [HBA1, HBA2]

Assessing variant c.37G>A (p.Gly13Ser) in HRAS; variant c.38G>A (p.Gly13Asp) in KRAS is established Pathogenic

Important to define mapping between genes!

Does Gly13 in HRAS = Gly13 in KRAS?

Slide30

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

≥2 different missense changes at AA residue have been seen before

PM5_Strong

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

General modifications for PM5:

Allow PM5 to be upgraded to Strong (PM5_Strong) if ≥2 different pathogenic missense changes at the residue have been seen before

Slide31

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

≥2 different missense changes at AA residue have been seen before

PM5_Strong

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

General modifications for PS1:

Can also be used for splice site variants

Slide32

PS1: Splice Site VariantsExample: You are assessing IVS3+5G>T

and IVS3+5G>

A

meets criteria for established pathogenic and has been showed to impact splicing in a functional assay. IVS3+5G>

T

has not been studied functionally but in

silico

splicing predictions show IVS3+5G>

T is equally or more damaging than IVS3+5G>A =

PS1 metIf in the same scenario (with IVS3+5G>A meeting criteria for established pathogenic and has been showed to impact splicing in a functional assay)

silico splicing predictions suggest IVS3+5G>T is not as damaging as

IVS3+5G>A = PS1 not metIf PS1 is met in these instances, PP3 (in silico prediction) would NOT be applied

Slide33

Multiple lines of comp evidence suggest no impact

BP4

Missense when only truncating cause disease

BP1

Silent variant w/ non predicted splice impact

BP7

In-frame indels in repeat w/out known function

BP3

Multiple lines of computational evidence support a deleterious effect on the gene /gene product

PP3

Predicted

null variant in a gene with moderate level of evidence for LOF as a disease mechanism

PVS1_Moderate

Missense change at an AA residue where a different pathogenic missense change has been seen before

PM5

Protein length changing variant

PM4

≥2 different missense changes at AA residue have been seen before

PM5_Strong

Same AA change as an established path variant

PS1

Predicted null variant in a gene where LOF is a known mechanism of disease

PVS1

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

COMPUTATIONAL AND PREDICTIVE DATA

General modifications for PVS1:

Can be downgraded to Moderate if:

LOF is not an established disease mechanism

Only moderate level of evidence for gene/disease pair, but all the evidence supports LOF as the disease mechanism

Slide34

De novo

(without paternity & maternity confirmed)

PM6

De novo

(paternity & maternity confirmed)

PS2

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

DE NOVO DATA

Slide35

DE NOVO DATA

Example:

Patient had a de novo missense variant in MECP2 but only presented with ID – no Rett phenotypes

Slide36

De novo

(without paternity & maternity confirmed)

PM6

De novo

(paternity & maternity confirmed)

PS2

≥2 De novo occurrences

(without paternity & maternity confirmed)

PM6_Strong

≥2 De novo

occurrences (paternity & maternity confirmed)

PS2

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

DE NOVO DATA

For PS2 and PM6, can increase strength with increasing independent de novo occurrences

Slide37

Observed in

trans

with a dominant variant

or

Observed in

cis

with a pathogenic variant

BP2

For recessive

disorders, detected

in trans with a

pathogenic variant

PM3

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

ALLELIC DATA

For PM3, shift weight according to variant strength and number of occurrences

Slide38

Observed in

trans

with a dominant variant

or

Observed in

cis

with a pathogenic variant

BP2

For recessive

disorder,

b

iallelic variants but variant on the other allele does

not meet pathogenic criteriaPM3_Supporting

For recessive

disorders, detectedin trans with a

pathogenic variantPM3

For recessive

disorders, ≥2 occurrences when detectedin trans with a

pathogenic variantPM3_Strong

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

ALLELIC DATA

Supporting:

Variant on the other allele “suspicious” and absent from control

dbs

OR

Proband homozygous for the variant and variant absent from control

dbs

Strong:

≥2 unrelated probands compound het with different pathogenic

variants in trans

Proband 1:

p.H308fs

;p.Y3955X

Proband 2:

p.H308fs

;p.N405fs

Proband 3:

p.H308fs

;p.N405fs

Slide39

Reputable source = benign

BP6

Reputable source = pathogenic

PP5

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

OTHER DATABASES

Slide40

Reputable source = benign

BP6

Reputable source = pathogenic

PP5

Strong

Strong

Very Strong

Moderate

Supporting

Supporting

Benign

Pathogenic

OTHER DATABASES

CRITERIA SHOULD NOT BE USED

Slide41

Move to Bayes ApproachACMG/AMP criteria are compatible with this quantitative approach

Slide42

Allow us to make better definitions for VUS and when Pathogenic and Benign data conflict(PVS# + PM# + PM#) + BP#

=

Pathogenic

(PS# + PS#) + BS#

=

Uncertain significance

Move to Bayes Approach