Disclosures Old, the New, and the Controversial I have no relevant - - PowerPoint PPT Presentation

6/6/2014 1

Genetic Carrier Screening: Review of the Old, the New, and the Controversial

Brian L Shaffer, MD

6/6/14 Assistant Professor Division of Maternal Fetal Medicine Oregon Health and Sciences University

Disclosures

• I have no relevant financial relationships

Objectives

• Carrier Screening: Review tenets
• ACOG recommendations – Ethnicity based screening
• Cystic Fibrosis, Hemoglobinopathies, Ashkenazi Jewish

Disorders, Fragile X, Spinal Muscular Atrophy

• Expanded carrier screening: “Universal”
• Pros and Cons
• What to expect

Carrier Screening - Foundation

Independent of family history: Asymptomatic Single gene: autosomal recessive; X-linked Informed consent: Non-directive

• Natural history of disorder - Severity
• Access to quality genetic counseling - Residual risk
• Acceptance by screened population - Voluntary

High frequency of carriers in screened population

• Geographic ancestry – 1 in 30

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Carrier Screening - Foundation

Quality test:

• Timely and dependable
• Inexpensive/cost efficient
• High detection rate – 90%

Availability of intervention: Preconception/Prenatal

• Donor sperm/egg; PGD; adoption; forgo pregnancy
• Prenatal diagnosis – To carry (and prepare) or not?

Goal: Risk assessment, informed decision making Public health implications: Prevention

Case 1 19 year old G1 8 wks, presents for new OB visit

• Ethnicity?
• Geographic ancestry?
• Her partner is from Mexico
• No family history of any

genetic disease

• In either she or FOB
• Carrier Screening

Case 1 19 year old G1 8 wks, presents for new OB visit

• Ethnicity?
• Geographic ancestry?
• Her partner is from Mexico
• No family history of any

genetic disease

• In either she or FOB
• Carrier Screening

Case 1 19 year old G1 8 wks, presents for new OB visit

• Ethnicity?
• Geographic ancestry?
• Her partner is from Mexico
• No family history of any

genetic disease

• In either she or FOB
• Carrier Screening
• “ACOG says”

ACOG SAYS ?

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Case 1 19 year old G1 8 wks, presents for new OB visit

• Ethnicity?
• Geographic ancestry?
• Her partner is from Mexico
• No family history of any

genetic disease

• In either she or FOB
• Carrier Screening
• “ACOG says”
• Cystic Fibrosis

ACOG SAYS ?

Cystic Fibrosis - CFTR

• Most common AR disorder among whites (1/2500-3300)
• 1/25-29 with no family history is a carrier of a CF gene change

(mutation) or variant alters function

• Pulmonary disease, pancreatic insufficiency, gastrointestinal,

infertility; normal intelligence

• Life limiting – ~40 years
• ~80% of children with CF are born to parents with no prior

family history of the disease

• ACOG: “it is difficult to assign a single ethnicity to affected

individuals… offer to all patients”

ACOG Committee Opinion #486, 2011

Case 1 (cont.) 19 year old G1 8 wks, presents for new OB visit

• Carrier Screening – negative for 32 mutations
• Carrier screening for a gene is needed only once
• “So my baby won’t have cystic fibrosis”
• What is a residual risk?
• What is the risk of having an affected child?

Group Incidence Carrier risk Detection Residual risk after negative

Ashkenazi 1/2270 1/24 94% 1/384 Caucasian 1/2500 1/25 88% 1/206 Hispanic 1/13,500 1/58 72% 1/203 African American 1/15,100 1/61 64% 1/171 Asian American 1/35,100 1/94 49% 1/183

Cystic Fibrosis: Incidence, Carrier risks and Detection rates*

* Detection rates derived from using ACMG 23 mutation panel

6/6/2014 4 Case 1 (cont.) 19 year old G1 8 wks, cystic fibrosis screening

• Patient: Carrier screening Negative for mutations tested
• Pre-test risk: 1/25
• After negative test: ~1/206 – (Residual Risk)
• Partner: No test
• Pretest partner carrier risk: 1/58 (Latin ancestry)
• Risk of affected fetus is:

(Mom) 1/206 x (FOB) 1/58 x (Fetus inheriting both) 1/4 = 47,000

Limitations of Cystic Fibrosis carrier screening

• Negative mutation analyses “reduce but do not eliminate” the

chance of having an affected child

• >1700 disease causing mutations for CF
• Mutations tested: those most frequently detected in disease
• Mutation frequencies vary in different ethnic/racial bkgd
• Sequencing of CFTR gene & deletion/duplication studies
• Residual risk estimate applies when:
• Family history is negative
• Correct Paternity

CF – What to do?

• Offer screening for CF to all women:
• Briefly…..
• Describe phenotype
• Describe inheritance
• Why women test?
• Describe limitations of testing
• If negative “substantially reduces risk of an affected child”
• Offer partner screening after discussion of results
• Document discussion
• Provide written materials
• … Offer formal GC if patient has additional questions

Hemoglobinopathies: “ACOG says”

African

ACOG Practice Bulletin #78, 2007

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Structure of hemoglobin

b1 b2 a1 a2 a3 a4

Beta globin genes Alpha globin genes Chromosome 11 Chromosome 16 Hemoglobin protein

Hemoglobinopathies: “ACOG says”

African

• Hemoglobin electrophoresis
• CBC

ACOG Practice Bulletin #78, 2007

ACOG SAYS ?

Hemoglobinopathies: “ACOG says”

African

• Hemoglobin electrophoresis
• CBC

ACOG Practice Bulletin #78, 2007

Hemoglobinopathies: “ACOG says”

African

• Hemoglobin electrophoresis
• CBC

Mediterranean

• CBC
• If Anemia, MCV <80 (microcytic)
• Normal iron studies (ferritin)
• Hemoglobin Electrophoresis
• Assess for Beta Thalassemia

ACOG Practice Bulletin #78, 2007

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Hemoglobinopathies: “ACOG says”

African

• Hemoglobin electrophoresis
• CBC

Mediterranean, Southeast Asian

• CBC
• If Anemia, MCV <80 (microcytic)
• Normal iron studies (ferritin)
• Hemoglobin Electrophoresis
• Assess for Beta Thalassemia
• If normal Beta and SE Asian
• α thalassemia

ACOG Practice Bulletin #78, 2007

ACOG SAYS ?

Hemoglobinopathies: Comprehensive screening

β thalassemia α thalassemia

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Hemoglobinopathies: Comprehensive screening

β thalassemia α thalassemia

Hemoglobinopathies: Comprehensive screening

β thalassemia α thalassemia

Hemoglobinopathies: Comprehensive screening

β thalassemia Latin, Middle Eastern, Indian, Pacific Islander, Chinese

• If Anemia, MCV <80, normal iron
• Hemoglobin Electrophoresis

α thalassemia Mediterranean (Italy, Greece), East Asia (China), Mid Eastern (Turkey, Pakistan), Central Asia (West India), African

• If Anemia, MCV <80, normal iron
• Hemoglobin Electrophoresis nl
• Molecular studies for alpha thal

Case 2

• 26 yo G1P0 at 10 weeks with a younger brother

with autism and cognitive disability who “looks different” than other family members. On further questioning her mother had early menopause.

• What is her fetus at risk for?
• Why the primary ovarian deficiency in her mother?
• What carrier screening should be offered?

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Case 2

• 26 yo G1P0 at 10 weeks with a younger brother

with autism and cognitive disability who “looks different” than other family members. On further questioning her mother had early menopause.

• What is her fetus at risk for?
• Why the primary ovarian deficiency in her mother?
• What carrier screening should be offered?

ACOG SAYS ?

Fragile X Syndrome

• Heritable cognitive disability, behavior
• Males (1 in 3600-4000)
• 2nd most common form of cognitive disability
• Behavior abnormalities
• Unique facial characteristics
• Females (1 in 4000-8000)
• If affected, usually less severe
• Primary ovarian deficiency
• Cognitive abnormalities
• Tremor ataxia

Fragile X – Who is at risk?

• Family h/o Fragile X or

undiagnosed cognitive disability

• Known maternal premutation or

full mutation

• Women with h/o elevated FSH or

primary ovarian insufficiency of unknown etiology

• Family h/o primary ovarian

insufficiency, tremor/ataxia

• Those with intermediate alleles

are not at risk of having an affected child

Mutation type CGG trinucleotide repeats Risk of Transmission to full mutation Methylation status (FMRI)

Phenotype

Men Women Normal <40 None Unmethylated Intermediate 41-60 Risk of transmission at 56 repeats Unmethylated Premutation 60-200 Yes Increases with repeat number Unmethylated At risk for FXTS (17% by age 60) At risk for FXTS and POF (POF risk 21%) Full Mutation >200 Approximately 100% Methylated Fragile X syndrome 100% with cognitive disability 50% with normal intellect; 50% with cognitive disability

Fragile X CGG repeat expansion, risks and clinical phenotype

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Mutation type CGG trinucleotide repeats Risk of Transmission to full mutation Methylation status (FMRI)

Phenotype

Men Women Normal <40 None Unmethylated Intermediate 41-60 Risk of transmission at 56 repeats Unmethylated Premutation 60-200 Yes Increases with repeat number Unmethylated At risk for FXTS (17% by age 60) At risk for FXTS and POF (POF risk 21%) Full Mutation >200 Approximately 100% Methylated Fragile X syndrome 100% with cognitive disability 50% with normal intellect; 50% with cognitive disability

Fragile X CGG repeat expansion, risks and clinical phenotype ACOG SAYS ?

Fragile X – Carrier Rate – “ACOG says”

• Low risk women (neg family history)
• 1 in 113-300
• Family history of Fragile X
• 1 in 4 (28.8%)
• Suspicious family history
• 1 in 83
• 1º ovarian insufficiency, ↑ FSH
• As high as 1 in 10

ACOG: No, but if requests, Yes, +GC ACOG: Yes, +GC ACOG: Yes, +GC ACOG: Yes, +GC

ACOG Committee Opinion #469, 2010

Case 3 25 year old G1, new OB

• Ashkenazi descent

Case 3 25 year old G1, new OB

• Ashkenazi descent

ACOG SAYS ?

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Case 3 25 year old G1, new OB

• Ashkenazi descent – “ACOG says”
• CF, Tay Sachs, Fam Dysautonomia, Canavan
• Others: “made available”

Case 3 25 year old G1, new OB

• Ashkenazi descent – “ACOG says”
• CF, Tay Sachs, Fam Dysautonomia, Canavan
• Others: “made available”

Case 3 25 year old G1, new OB

• Ashkenazi descent – “ACOG says”
• CF, Tay Sachs, Fam Dysautonomia, Canavan
• Others: “made available”
• Tay Sachs – “ACOG says”
• AJ, Fr Canadian (Quebec), Cajun
• Leukocyte testing in pregnancy –
• Biochemical
• Carrier screening
• Refer

ACOG Committee Opinion #442, 2009 ACOG Committee Opinion #318, 2005

Disorder Disease incidence Carrier frequency Detection Rate

Tay-Sachs† Canavan† Familial dysautonomia† Cystic fibrosis† Fanconi anemia- group C Niemann-Pick- type A Mucolipidosis- type IV Bloom Gaucher 1/3,000 1/6,400-9,100 1/3,600 1/2,500-3,000 1/32,000 1/32,000 1/62,500 1/40,000 1/900 1/30-31 1/40-48 1/31-32 1/24-29 1/89 1/90 1/127 1/107 1/15-18 98% by HEX A enzyme 92-99% by DNA 98% 99% 94-97% 98-99% 94-97% 90-95% 99% 89-95% French Canadian/Cajun† Tay-Sachs 1/675-360,000 1/13-300 Varies

Table 1-1. Ashkenazi Jewish/East European – Geographic Ancestry-based Carrier Screening † - ACOG recommends

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Case 4 35 year old G1, IVF Case 4 35 year old G1, IVF, requests SMA screening Case 4 35 year old G1, IVF, requests SMA screening

ACOG SAYS ?

Case 4 35 year old G1, IVF, requests SMA screening

Spinal Muscular atrophy (SMA), SMN1

• 2nd most common fatal recessive disease
• All ethnicities, 1 in 40-60
• Motor weakness, paralysis, death - weakness – variable
• Education, counseling – logistics, phenotype & genetics
• Patient preferences, cost effectiveness

“ACOG says” – No, unless request and have formal GC Expanded carrier screening?

ACOG Committee Opinion #432, 2009

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Expanded Carrier screening: Why?

• All are carriers of recessive conditions – up to 7 diseases
• Ethnicity based screening has limitations:
• Difficult to appropriately assign ethnicity (e.g., CF)
• Does not identify all who may want prenatal diagnosis
• Technology -- Next generation sequencing
• Quick, inexpensive, high fidelity identification of mutations
• Screen many genes for disease causing mutations
• Test ~100 genes for known mutations (~400)
• No longer, what can we screen for?
• but what should we screen for?

Expanded carrier screen: Controversy

Issue Potential Solution Which diseases?

• Severity
• Organ affected
• Milder phenotype
• Adult in onset

ACMG Policy Statement, Genet Med 2013

Expanded carrier screen: Controversy

Most patients at risk: Consider PNDx Mild phenotype Variable expressivity Incomplete penetrance

• - Optional

Adult onset Could impact his/her offspring

• - Must provide consent

Issue Potential Solution Which diseases?

• Severity
• Organ affected
• Milder phenotype
• Adult in onset

ACMG Policy Statement, Genet Med 2013

Expanded carrier screen: Controversy

Issue Potential Solution For a given disorder:

• Causative gene
• Mutation
• Frequencies

Residual risk calculation Carrier frequency Allele frequency Risk is less? By how much Doctor?

ACMG Policy Statement, Genet Med 2013

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Expanded carrier screen: Controversy

Laboratories Report residual risk How risk was calculated High detection rate Issue Potential Solution For a given disorder:

• Causative gene
• Mutation
• Frequencies

Residual risk calculation Carrier frequency allele frequency Risk is less? By how much Doctor?

ACMG Policy Statement, Genet Med 2013

Expanded carrier screen: Controversy

Issue Potential Solution Quality test Genotype-Phenotype For a mutation

• Mild-severe?
• Variant?

ACMG Policy Statement, Genet Med 2013

Expanded carrier screen: Controversy

Laboratories should provide citation regarding the typical clinical course Issue Potential Solution Quality test Genotype-Phenotype For a mutation

• Mild-severe?
• Variant?

ACMG Policy Statement, Genet Med 2013

Expanded carrier screen: Controversy

Issue Potential Solution Informed consent can’t be obtained

ACMG Policy Statement, Genet Med 2013

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Expanded carrier screen: Controversy

Alter process Undergo general pre-test counseling for both partners Detailed post test counseling Risk 1 in 4 Residual risk Issue Potential Solution Informed consent can’t be obtained

ACMG Policy Statement, Genet Med 2013

Expanded carrier screen: What to expect

• ~25% – carrier one or more conditions
• ~0.7% of couples have changes in the same gene
• CF, SMA, Smith-Lemli-Opitz syndrome, Connexin 26
• Option of invasive testing
• May find that your patient or father of the baby has “disease”
• Incorrect classification of a “mutation”
• Reduced penetrance or variable expressivity

Expanded carrier screen: What to do

• Prepare patients for potential results
• Preconception period, if possible
• Well woman Gyn visit
• Preconception visit
• Perform only once
• Formal genetic counseling
• In person, phone, telemedicine

Summary

ACOG: Ethnicity based carrier screen All women: CF African: Hgb Elec, CBC SE Asian, Mediterranean – CBC, <80; Hgb Elec – β thalassemia SE Asian – α thalassemia Family/Personal history for FraX – carrier screen +GC Ashkenazi – CF, TSD, Canavan, Fam dysautonomia French Canadian, Cajun – TSD “I want SMA testing” GC and SMA Be prepared for expanded carrier screening

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Thank you

ACOG SAYS ?

References

1) Carrier Screening Based on Ashkenazi Jewish Ancestry: ACOG committee opinion

• no. 442: preconception and prenatal carrier screening for genetic diseases in

individuals of Eastern European Jewish descent, 2009 . 2) Carrier Screening for Hemoglobinopathies American College of Obstetricians and Gynecologists Committee on Obstetrics : ACOG practice bulletin no. 78 Hemoglobinopathies in pregnancy , 2007. 3) Carrier Screening for Cystic Fibrosis Committee on Genetics: ACOG committee

• pinion no. 486: Update on carrier screening for cystic fibrosis, 2011.

4) ACOG committee opinion no. 469: carrier screening for fragile X syndrome, 2010. 5) ACOG committee opinion no. 432: Spinal muscular atrophy, 2009 . 6) ACOG committee opinion no. 318: Screening for Tay-Sachs disease, 2005 . 7) Grody WW, et al; ACMG Policy Statement: ACMG position statement on prenatal/preconception expanded carrier screening; Genet Med 2013.

Heterozygote (Carrier) screening and “ethnicity” or geographic ancestry

All women Cystic fibrosis Ashkenazi Jewish Tay-Sachs, Canavan disease, familial dysautonomia, make “other” available African American, African, Mediterranean Sickle cell anemia

Ethnic group Disease

Heterozygote (Carrier) screening and “ethnicity” or geographic ancestry

Southeast Asian, Mediterranean, African (not African American), Middle Eastern, Indian, Chinese Alpha thalassemia Mediterranean, East Asian, Middle Eastern, Central Asia, Far Eastern Beta thalassemia All ethnicities? Spinal muscular atrophy Expanded carrier screening Ethnic groups Disease

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DNA REPORT Cystic Fibrosis Ethnicity: White: Non-Hispanic Supplemental indications: Supervision of Other Normal Pregnancy Patient Results: Negative for mutations analyzed Interpretation: It is our understanding that this individual has a negative personal and family history of cystic fibrosis (CF). Using the methodology described, this individual is negative for the 23 CF mutation screening test recommended by the American College of Medical Genetics. These results do not rule out the possibility that this individual could be a carrier of a mutation not detected by this test. The following table provides data to be used in the genetic counseling for this individual. Limited information is available for individuals from other ethnic groups. These risks would differ for individuals who have a family history of CF; if this is the case for this patient, please contact the laboratory. Estimated Carrier Risk ETHNIC GROUP DETECTION RATE BEFORE TEST AFTER NEG TEST Ashkenazi Jewish 94% 1/24 ~1 in 384 European Caucasian 88% 1/25 ~1 in 206 African American 64% 1/61 ~1 in 171 Hispanic American 72% 1/58 ~1 in 203 Asian American 49% ~1/94 ~1 in 183 Methods: The CFTR gene was tested for the presence of these specific 32 mutations (and benign variants as indicated) by polymerase chain reaction (PCR) and oligoligation assay. The ACMG panel of 23 recommended mutations is shown as the standard mutation panel.