In the session of "Genetic testing 101" in APHRS 2019 The presentation slides for "Whom should be tested?"

1. Genetic Testing 101
Whom should be tested?
Yusuke EBANA
Tokyo Medical and Dental University
Department of Medical Genetics

2. Introduction: Inherited arrhythmia syndrome
• Long QT syndrome (LQTS)
• Brugada syndrome (BrS)
• Catecholaminergic polymorphic ventricular tachycardia (CPVT)
• Idiopathic ventricular fibrillation (IVF)
• Short QT syndrome (SQTS)
• Progressive cardiac conduction system disease（PCCD）

3. Collection and assessment of family history
information
• Know the purpose of testing
• Pedigree in 3-5 generation
• Proband with arrow
• Separate in 4:
1. history of syncope
2. Sudden cardiac death
3. Implanted ICD
4. LQTS/BrS Dx
• Start from family member with
severe cardiac event
• Recommend GT for first degree
relatives
Spoonamore KG et al. Heart Rhythm 2016;13:789-797

4. Collection and assessment of family history
information
• First degree relative of III-6:
II-2, II-3, III-7, IV-1, and IV-2
IV-5/6 may need to evaluate
If III-7 is positive, go to IV-3/4
• II-3 is negative and II-2 is
suspected to be positive
• II-1 is also suspected
• III-1, 2, 3, 4, 5 need to evaluate Spoonamore KG et al. Heart Rhythm 2016;13:789-797

5. Characteristics of genetic information
• Genetic information
1. does not change for a lifetime
2. Inherited to family
3. May be able to accurately predict the onset of disease
4. Enables to predict the family members who do not undergo
genetic testing
5. Enables to diagnose non-onset carrier
6. Can be a disadvantage for the person if handle improperly

6. When to test
• Individual who comes to be at risk should be recommended
• Those who can be at risk need to give information for
genetics
• Genetic information may have a large impact for healthy
member
• May be appropriate when transitioning care from pediatric to
adult providers
• retesting may be appropriate if the previous testing produced
negative or inconclusive results

7. Genetic testing with NGS:
• The development of NGS leads to large gene sequencing
panel
• Technically feasible and cost-effective
• To identify a molecular etiology with mixed phenotype
• Whole exome sequencing (WES) interrogates all coding
regions of every gene
• WES or whole genome sequencing may become tests of
choice in the future
• Interpretation of variants and incidental finding

8. Criteria for classifying pathogenic variants
ACMG Standards and Guidelines 2015
Genetics in Medicine 17;405-424
Interpretation of genetic variants:
• Pathogenic
1. Very strong null variants
2. Strong 1) Same amino acid changes as previously reported 2)
De novo in no family history 3) Well-established in vitro/in vivo
functional study 4) compared with prevalence in control
3. Moderate 1) Mutational hot spot, 2) absent from controls, 3)
Fro recessive disorders detected in trans 4) Protein length
change 5) missense change of pathogenic amino acid change
without previous mutation
4. Supporting 1) cosegregation with disease in multiple affected,
2) missense variant in low rate in general 3) computational
evidence 4) Specific phenotypes 5) Reputative source

9. Criteria for classifying pathogenic variants
ACMG 2015
Genetics in Medicine 17;405-424
Interpretation of genetic variants:
• Benign
1. Stand-alone Allele Frequency > 5%
2. Strong 1) greater allele frequency, 2) Observed in healthy
adult individual, 3) Well-established in vitro/in vivo study 4)
Lack of segregation
3. Supporting 1) Missense variant with known to cause
disease, 2) Observed in trans, 3) In-frame del/ins in
repetitive region 4) computational evidence… and so on

10. Rules for combining criteria:
for example; “pathogenic”
e.g.
Pathogenic
(i) 1 Very strong (PVS1) AND
(a) ≥1 Strong (PS1–PS4) OR
(b) ≥2 Moderate (PM1–PM6) OR
(c) 1 Moderate (PM1–PM6) and 1 supporting (PP1–PP5) OR
(d) ≥2 Supporting (PP1–PP5)
(ii) ≥2 Strong (PS1–PS4) OR
(iii) 1 Strong (PS1–PS4) AND
(a)≥3 Moderate (PM1–PM6) OR
(b)2 Moderate (PM1–PM6) AND ≥2 Supporting (PP1–PP5) OR
(c)1 Moderate (PM1–PM6) AND ≥4 supporting (PP1–PP5)

11. Expert panel in TMDU consists of
• Clinical cardiologist in department of cardiology
• Clinical geneticist in department of medical genetics
• Basic researcher for ion channel
• Basic researcher for GWAS
• Certified genetic counsellor
• Interpretation for variant; pathogenic, likely pathogenic, likely
benign, benign, VUS
• Evaluation of evidence for basis research data
• The function of variant

12. Genetic conference in TMDU
• All the medical geneticist
• discuss the cases including variants and
• determine genetic counseling plan
• Report case
• Member:
• Clinicians in various department such as family medicine, internal medicine,
pediatrician, gynecologist, and others
• Clinical Geneticist in department of medical genetics
• Basic Researcher
• Certified Genetic Counsellor
• Nurse
• Other institute/hospital member

13. Genetic counseling after genetic testing
• Includes the result, variant interpretation, and treatment/management
• Risk stratification
• Explanation of molecular basis if needed
• Objective: proband, family members including the first degree relatives
and spouse
• The decision-making of treatment, e.g. ICD or medication, we work
closely with clinical cardiologist
• VUS problem
• Negative result does not rule out an inherited arrhythmia syndrome

14. Summary
• Family history collection and making family tree
• Characteristics of genetic information
• Variant interpretation
• Expert panel and genetic conference
• Genetic counseling with certified genetic counselors