Faculty/Presenter Disclosure Faculty: Dr. June Carroll Program: 51 st Annual Scientific Assembly...

Faculty/Presenter DisclosureFaculty/Presenter Disclosure

• Faculty: Dr. June Carroll• Program: 51st Annual Scientific Assembly

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• This program has received NO financial support • This program has received NO in-kind support

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• Faculty: Dr. Judith Allanson• Program: 51st Annual Scientific Assembly



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Genomics and Primary Care:Are you ready?

June C. Carroll MD CCFP FCFPSydney G. Frankfort Chair in Family Medicine

Associate Professor and Clinician ScientistDepartment of Family & Community Medicine

Mount Sinai Hospital, University of Toronto

Sean Blaine MD CCFP FCFPAssistant Professor, Department of

Family & Community MedicineUniversity of Toronto

STAR Family Health Team

Judith Allanson MB ChB FRCP(C) FCCMGProfessor Emeritus

Children’s Hospital of Eastern OntarioUniversity of Ottawa

Shawna Morrison MS CGCCertified Genetic Counsellor and

Program Manager of GEC-KOChildren’s Hospital of Eastern Ontario

Hereditary Hemochromatosis (HH)

Genomics and Primary Care SeminarNovember 2013

Case• Michael is a 49-year-old male of Northern European descent

with complaints of joint pain in his knees and hands. He is having a difficult time because his brother recently passed away at a young age.

• Past Medical History:– Numerous office visits over 3–4 years for fatigue, weakness, and pain

• Family History:– Michael is married with two healthy teenage sons (16, 14)– Father died at age 55 from myocardial infarction (MI)– Mother, 76, alive and well– Brother died at age 53 of esophageal varices – Sister, 55, has type II diabetes – Brother, 43, and sister, 40, alive and well

CDC- NCBDDD http://www.cdc.gov/ncbddd/hemochromatosis/index.html

Family history

4055

43d.53

16

MI

55 75

14

49

Esophageal varices Type II diabetesJoint pain – knees and handHPI fatigue, pain & weakness

A&W

A&W A&W

Case

• Social History:– Drinks "a couple of beers a week”, no tobacco or recreational drug use– No multivitamin use

• Physical Exam:– Mild hepatomegaly– Modest enlargement of the second and third MCP joints

What is HH?• HH is an inherited predisposition to absorb excess iron (Fe) from

the diet• Mutations in the HFE gene are the most common cause of adult

onset iron overload• In some predisposed individuals, excessive iron absorption and

subsequent storage in various organs (i.e. liver, pancreas, heart, joints) eventually lead to cellular injury

• If untreated, over time this can cause irreversible tissue/organ damage and shorten life expectancy

• With early identification of at-risk individuals, surveillance of iron indices, and treatment when necessary, all complications can be avoided

What is HH?• Typically, symptoms of HH present in men aged 40-60 and in post-

menopausal women; however, onset is variable and can occur much earlier or much later.

• Symptoms are nonspecific and include:– weakness, lethargy – skin discoloration (bronze or grey) – abdominal pain with or without hepatomegaly – joint pain and/or stiffness, arthritis – diabetes – cardiomyopathy– cirrhosis– hepatocellular carcinoma

– testicular atrophy, impotence– menstrual irregularity

While any of these health concerns can be caused by HH, the presence of two or more should greatly increase suspicion that the condition is present

What do I need to know about the genetics of HH?

• Autosomal recessive, with reduced penetrance • Caused by mutations in the HFE gene located on chromosome 6• Standard testing by North American molecular genetics laboratories

is targeted mutation analysis– Looks specifically for the two most common HFE mutations, C282Y

and H63D – These account for over 90% of HH

• About 1 in 3 individuals of Northern European ancestry are carriers (heterozygotes) of the C282Y or H63D HFE gene mutations

• About 1 in 260 individuals have two copies of (are homozygous for) the C282Y HFE gene mutation (genotype C282Y/C282Y)

AR Inheritance Refresher

C282Y / H C282Y / H

C282Y carrier

C282Y/ H

C282Y carrier C282Y carrier

H/ H C282Y/ C282Y

Homozygous for C282Y

At risk for iron overloadActual risk depends on other genetic and not genetic factors

No HFE gene mutation C282Y carrier

H / C282Y

¼ - 25%

¼ - 25%

½ - 50%

C282Y / C282Y H / H

C282Y/ H

Homozygous for C282Y No HFE mutation

C282Y/ H C282Y/ HC282Y / H

100% will be heterozygous for C282Y HFE mutation *can reveal non-paternity

AR Inheritance

Who should be offered biochemical testing for iron overload?

• If your patient has suggestive symptoms, physical findings or a family history of HH, transferrin saturation and serum ferritin are ideally ordered together to determine the likelihood of iron overload.

• Transferrin saturation (TS)– TS is a reliable screen for iron overload – Fasting TS of >45% is considered a sensitive but not specific threshold for identifying

individuals who may have iron overload.

• Serum ferritin (SF)– In combination with persistent elevation of fasting TS, elevated ferritin is suspicious for

iron overload. – Remember that SF is an acute phase reactant that can be elevated by other

inflammatory processes. Therefore an elevated SF does not necessarily imply iron overload and is not a reliable first or only screen.

Who should be offered genetic testing?• Any adult with biochemical evidence of iron overload

– >45% transferrin saturation (TS) and >300g/L serum ferritin (SF) in men and post-menopausal women or >200g/L SF in pre-menopausal women

• Unexplained chronic liver disease and increased TS• An adult with a first-degree relative (sibling, parent or child) with one of the following

genetic test results:– C282Y/C282Y (homozygote)– C282Y/H63D (compound heterozygote)– C282Y/S65C (compound heterozygote)– C282Y heterozygote (carrier)

• Family history of iron overload, liver disease, type II diabetes, arthritis, heart disease (relatives with symptoms of HFE-HH)

Individuals with HFE-HH occasionally demonstrate a normal TS and an elevated ferritin. If

clinical suspicion is high and/or the patient has a family history of HFE-HH, genetic testing is still warranted

What does the genetic test result mean?

• The actual risk to develop iron overload is dependent on how many and which gene mutations have been inherited, in addition to other genetic and non-genetic factors– gender– alcohol intake– use of iron and vitamin C supplements – menstrual/pregnancy-associated iron losses

What does the genetic test result mean? • Two mutations identified confirm HH diagnosis in an individual with

biochemical evidence of iron overload.• Two mutations identified in an asymptomatic individual suggest risk of

developing iron overload and yearly monitoring of iron indices is recommended.

HFE mutations identified

Risk of iron overload

C282Y/C282Y Highest risk of developing iron overload (38-50%)

-Many of these individuals never accumulate enough iron to cause disease (about 10-33% may develop HH related symptoms )

C282Y/H63D About 2% lifetime risk of developing iron overload

C282Y/S65C Low lifetime risk of developing iron overload - similar to C282Y/H63D

H63D/H63D About 1% lifetime risk of developing iron overload

How do I order the genetic test?

• Genetic testing is performed on a blood sample– Will only assess risk to develop HH or confirm diagnosis in

symptomatic patient

• It is important to include the following information on any requisition for the best test interpretation:– Indication for testing e.g. ‘symptoms of indicated disease’ or ‘abnormal iron

indices’ or ‘positive family history’– Ethnicity e.g. Northern European – Relevant family history e.g. parent/sibling with HH (include genetic test results

of affected individual if known)– Relevant medical history/investigations; e.g. biochemical iron overload

How will genetic testing help you and your patient?

• If mutations are identified– Appropriate surveillance and management of risk of iron overload

• If no mutations are identified– If your patient was tested because of a known family mutation, he/she

no longer needs frequent monitoring of iron indices and is not at increased risk to develop iron overload. The test has ruled out HH.

– If your patient was tested because of a reported positive family history, more information is needed before ruling out HH in this individual. Your patient should be encouraged to obtain confirmation of the familial mutations and/or diagnosis.

– If your patient was tested because of persistently high iron indices, additional investigations should be considered

Are there harms or limitations of genetic testing?

• Potential harms – Insurance discrimination

• Genetic testing in an asymptomatic individual may affect his/her ability to obtain life, disability, critical illness, long-term care and/or extended health insurance.

• HH is a treatable condition and some insurance companies will not deny coverage to a treated individual

– Non-Paternity

• Limitation– Targeted mutation analysis

• Not every HFE gene mutation is looked for, however, the most common mutations account for more than 90% of all mutations, thus fewer than 10% will be missed using current testing strategies

Case

• Based on blood work demonstrating biochemical evidence of iron overload– Ferritin >300g/L AND TS >45%

• + suggestive family history [MI, liver disease with iron overload, type II diabetes in first degree relatives]

• You suspect HH and offer genetic testing• Michael accepts and the results show he is

homozygous for C282Y HFE gene mutation

Surveillance and management Patient identified to have two HFE

gene mutations

Normal Increased

Continue annual SF monitoring

Annual monitoring of serum

ferritin (SF)

Refer to specialist (e.g.

gastroenterologist, hematologist)

Pearls•HH is a common inherited predisposition to absorb excess iron from the diet caused by mutations in the HFE gene •Most individuals with the predisposition do not develop clinical disease •HH has the potential to cause morbidity and mortality. With early identification of at-risk individuals, appropriate surveillance of iron indices, and treatment when indicated, all complications can be avoided.•Genetic testing should be considered for:

– Adults with biochemical evidence of iron overload (>45% fasting transferrin saturation and >300g/L serum ferritin in men and post-menopausal women or >200g/L SF in pre-menopausal women)

– Any adult whose first-degree relative has the C282Y HFE gene mutation– Individuals with suggestive family histories

References• Bacon BR, Adams PC, Kowdley KV, Powell LW, Tavill AS, American Association for the Study of

Liver Diseases. 2011. Diagnosis and management of hemochromatosis: 2011 practice guideline by the American Association for the Study of Liver Diseases. Hepatology. 54:328–43

• European Association for the Study of the Liver. 2010. EASL clinical practice guidelines for HFE hemochromatosis. J Hepatol. 53:3–22

• GeneReviews. HFE-Associated Hemochromatosis. http://www.ncbi.nlm.nih.gov/books/NBK1440/ Updated April 19th, 2012 [Accessed October 2013]

• Wallace DF, Walker AP, Pietrangelo A, Clare M, Bomford AB, Dixon JL, Powell LW, Subramaniam VN, Dooley JS. 2002. Frequency of the S65C mutation of HFE and iron overload in 309 subjects heterozygous for C282Y. J Hepatol. 36(4):474-9.

• Centre for disease Control and Prevention. National Center on Birth Defects and Developmental Disabilities. Hemochromatosis. http://www.cdc.gov/ncbddd/hemochromatosis/index.html [Accessed September 2013]

Lynch syndrome (LS)


Case • Jane - healthy 26 y.o.• Office visit for a routine pap smear and renewal of

birth control pills• Family History (any cancer in the family?)

– Mother with breast cancer at 66– Father’s side of the family:

– uncle - CA kidney age 72– uncle - CA colon age 56– aunt - double primary: endometrial CA age 45, colon CA age 68– 1 cousin - endometrial CA age 40– 2 cousins - both have colon CA

Family history

Jane, 26Linda Dx 38 CA - colon

Jeana Dx 40 Ca-Endometrial

Christa Dx 52CA – Colon

Mary

Dx 45 CA Endometrial

Dx 68 CA Colon

Bob Dx 56CA colon

Steve Dx 72CA Kidney

Paula Dx 66CA- Br

MI 72

Accident Nat Causes Stroke A&W

A&W A&WA&W

A&W A&W

Kevin, 67A&W

LEGEND

Kidney

Colon

Endometrial

Breast

What is Lynch Syndrome?• Lynch syndrome (LS), also known as Hereditary Non-Polyposis

Colorectal Cancer, (HNPCC), is an inherited cancer predisposition syndrome

• Individuals with LS have a greatly increased risk for certain cancers

• One to 3% of CRC is attributable to LS

LYNCH SYNDROME-RELATED CANCERS Colorectal cancer Endometrial KidneyGastric Ovarian UreterSmall bowel Hepatobiliary PancreaticBrain Sebaceous (adenoma or carcinoma)

What do I need to know about the genetics of LS?

• Autosomal dominant• Reduced penetrance and variable expressivity

– not all individuals who inherit a mutation in a LS gene will develop cancer (reduced penetrance)

– signs and symptoms/type and onset of cancer will vary between affected family members (variable expressivity)

• Caused by an inherited mutation in at least one of four mismatch repair (MMR) genes* (MLH1, MSH2, MSH6 or PMS2)

• About 1 in 440 individuals are estimated to have inherited a mutation in a Lynch syndrome gene

Mismatch repair genes play an important role in a cell’s ability to repair DNA damage as a cell grows and divides by identifying and removing single nucleotide mismatches, insertions and deletion loops. Defects in the MMR pathway lead to an accumulation of mutations in a cell which may result in a malignancy

Who should be offered genetic testing?

• Currently the decision to offer genetic testing is made in the setting of a genetics consult at a Hereditary Cancer Program or a General Genetics Clinic

• If possible, the affected individual in the family at highest risk to carry a mutation is offered testing first in order to maximize the likelihood of detecting a mutation– This would usually be a young individual with CRC or associated cancer

Red Flags for Hereditary Cancer

• Multiple family members with cancer– Same side of family– Diagnosed at a young age– Several generations affected

• Clustering of cancers • Multiple primary cancers in same individual

Personal history Red Flags for a CRC syndrome

• An early age of CRC diagnosis (<50 years)– Patients diagnosed <35years are much more likely to have LS.

• An early age of endometrial cancer diagnosis (<50 years)• Multiple primary LS-related cancer diagnoses, regardless of age• CRC diagnosis with one or more 1st degree relatives with a LS-related

cancer, with one of the cancers being diagnosed <50 years• CRC diagnosis with two or more 1st or 2nd degree relatives with LS-

related cancers regardless of age• CRC diagnosis <60 years with histological features suspicious for LS (excess

infiltrating lymphocytes, mucinous/signet cell features, Crohn-like reaction), particularly when primary tumour is right-sided

LYNCH SYNDROME-RELATED CANCERS Colorectal Endometrial KidneyGastric Ovarian UreterSmall bowel Hepatobiliary PancreaticBrain Sebaceous (adenoma or carcinoma)

Family history Red Flags for a CRC syndrome

• A patient is considered to be at high risk for LS syndrome if he/she has:– At least three relatives with a LS- associated cancer; the

following criteria should also be present:• One must be a first degree relative of the other two;• At least two successive generations must be affected (autosomal

dominant inheritance);• At least one relative with LS-related cancer should be diagnosed

before age 50;

– Tumour pathology should be verified when possible and other CRC syndromes should be ruled out

Family history Red Flags for a CRC syndrome

• A patient is considered to be at intermediate risk for LS if he/she has:– A 1st or 2nd degree relative with CRC diagnosed before age

35– A 1st or 2nd degree relative with two or more LS-related

cancers – 2 or more 1st or 2nd degree relatives on the same side of

the family with CRC diagnosed before age 50– 3 or more relatives on the same side of the family with any

LS-related cancer diagnosed at any age, at least one of whom has CRC or endometrial cancer

What does the genetic test result mean?

• If your patient has been found to carry a mutation in a LS gene – he/she has an increased lifetime risk to develop

certain cancers – family members are at risk of carrying the same

mutation and of having similar cancer risks

Cancer type Lynch syndrome lifetime cancer risk (carrier of a MLH1 or MSH2 gene

mutation)

General Population lifetime cancer risk

to age 70

Risk Mean age at diagnosis

Risk

Colon 52-82% 44-61 years 5.5%Endometrium 25-60% 48-62 years 2.7%Stomach 6-13% 56 years <1%Ovary 4-12% 42.5 years 1%Hepatobiliary tract 1-4% Not yet reported <1%Urinary tract (ureter and renal pelvis)

1-4% 55 years <1%

Small bowel 3-6% 49 years <1%Brain/ central nervous system

1-3% 50 years <1%

Sebaceous neoplasm 1-9% Not yet reported <1%Pancreas 1-6% Not yet reported <1%

MLH1, MSH2, MSH6 OR PMS2 intact

Genetic testing on blood sample on

affected individual


affected individual

MLH1, MSH2, MSH6 OR PMS2 deficient

MSI high

MSI stable or low

Affected at risk individual

Affected at risk individual

CRC* tumour (*preferred

type)

CRC* tumour (*preferred

type)

MSI on tumourMSI on tumour

IHC analysisIHC analysis


affected individual


affected individual

No further testing

No further testing

Microsatellite instability (MSI)• An important concept in LS pathology• A microsatellite is an area of DNA with a repetitive sequence

(i.e. CGCGCGCGC or GAAGAAGAA)• These stretches of DNA are susceptible to acquiring errors

when a mutation in a MMR gene is present• Cancer arising as the result of a defective MMR gene exhibits

an inconsistent number of microsatellite repeats when compared to normal tissue - this is called microsatellite instability (MSI)

• Approximately 90% of CRCs occurring in individuals with Lynch syndrome exhibit MSI – Approximately 15% of sporadic cancers (not associated with LS) also exhibit

MSI

How do I order the genetic test?

• Genetic testing is generally performed on a blood sample

• Specifics will depend on your region. Details can be found at www.gecko-cegco.ca


Positive result:• Clinical intervention may improve outcome• Family members at risk can be identified• Positive health behaviour can be reinforced• Reduction of uncertaintyTrue negative:• Avoidance of unnecessary clinical interventions• Emotional - relief• Children can be reassured


Positive result:• Adverse psychological

reaction• Family issues/distress• Uncertainty -incomplete

penetrance• Intervention may carry risk• Discrimination

– Job, insurance

• Privacy, confidentiality

True negative:•Adverse psychological reaction (i.e. survivor guilt)•Dysfunctional family dynamics•Complacent attitude to healthUncertain result:•Complacent attitude to health•Uncertainty•Continued anxiety

Screening and surveillance

• For patients who have a known mutation in a LS gene, the genetics healthcare provider or oncologist should provide recommendations specific to the patient and his/her family history

Screening and surveillance• In general, for high risk individuals with MLH1 or MSH2

mutations and their first degree relatives who have not had genetic testing:

• Colon Cancer– Colonoscopy every 1-2 years beginning between ages 20 and 25 or 2-5 years

prior to the earliest diagnosis if that diagnosis was made before age 25 years, whichever is earlier

• Endometrial and Ovarian cancer– There is no specific screening for endometrial or ovarian cancer – Educate women about symptoms of endometrial cancer– Prophylactic hysterectomy and bilateral salpingo-oophorectomy (BSP) is a risk-

reducing option that women who have completed childbearing can consider

• Other Extracolonic cancers– Family history dependent


• CRC screening for intermediate risk individuals (based on family history)

NCCN, 2012

• For patients who are at general population risk, including those who have tested negative for a known familial CRC gene mutation, recommendations should follow provincial guidelines– i.e. Fecal Occult Blood Test q2 years from age 50


• Pearls• Lynch syndrome (LS) is the most common hereditary colon

cancer predisposition syndrome• It is an autosomal dominant condition that results in an

increased lifetime risk of colorectal cancer (CRC) in addition to other cancers

• Individuals at high or intermediate risk of LS should be referred for a genetic consultation for consideration of genetic testing

• Surveillance and management of CRC and other cancers should be guided by genetic test results and/or family/ personal history – Studies show that conversations between patients and their healthcare

providers are the strongest driver of screening participation

References• Leddin, D et al., 2004. Canadian Association of Gastroenterology and Canadian

Digestive Health Foundation: Guidelines on colon screening. Can J Gastroenterol. 18(2): 93-99

• Lynch HT et al., 2009. Review of the Lynch syndrome: history, molecular genetics, screening, differential diagnosis, and medicolegal ramifications. Clin Genet 76(1):1-18.

• GeneReviews. Lynch Syndrome. http://www.ncbi.nlm.nih.gov/books/NBK1211/ Updated September 20, 2012

• National Comprehensive Cancer Network (NCCN). 2012. Guidelines for colon cancer screening. [Login required – no fee] http://www.nccn.org/professionals/physician_gls/f_guidelines.asp#colorectal_screening

Autism and Developmental Delay


CaseYou have known the Spencer family for several years. They have a 4 year old daughter, Alice, who is healthy and very bright. Their son, Aidan, was born 2 years ago. He is an attractive boy with normal stature and a slightly large head. During his first year, his parents noticed that, compared to his sister, he was floppy, with more balance and coordination difficulties; he did not establish a sleep pattern well and had lots of early morning wakening. He is a very busy boy and seems hypersensitive to noise. They are most concerned about delayed language acquisition that is becoming more obvious as time passes.

Family history

The Spencers, their siblings and parents are all healthy. Aidan

•Floppy•Balance & coordination difficulties•Difficulty establishing sleep pattern•Hypersensitive to noise•Language delay

4 2

AliceA&W

BrettA&W

BeverlyA&W

BrendaA&W

BarbA&W

BenjaminA&W

CarlA&W

CathyA&W

CameronA&W

CoralA&W

What is autism?

• Persistent deficits in communication and social interaction, and repetitive, restricted behaviours and/or interests

• There is wide variability within the “spectrum” (autism spectrum disorder, ASD) and affected individuals may have average intelligence or mild to severe intellectual disability

• note: diagnosis of autism is out of scope for this workshop

What do I need to know about the genetics of autism spectrum?

• ASDs are considered genetically influenced neurodevelopmental disorders with evidence pointing to dysfunction at the level of the synapse

• There is extensive genetic heterogeneity and perhaps hundreds of genetic variants involved

• A specific genetic etiology can be found in about 15% of individuals with a diagnosis of ASD

• Newer genetic testing modalities may increase yield to 30-40%

Identifying genetic causes of autismTest Pick up rate

Chromosomal microarray (CMA)* ~10-20% of children with ASD will be found to have a chromosomal microdeletion or microduplication (Copy Number Variant [CNV])

Fragile X syndrome testing [FMR1 gene testing]20% of boys with FXS meet the diagnostic criteria for autism

1-6%

Other rarer single gene conditions [testing a specific gene] or chromosome differences that may be seen on karyotype

5%

Metabolic <1%

CMA• CMA is a technology used to determine if there are small extra (microduplication)

or missing (microdeletion) pieces of genetic information. These gains and losses are called copy number variants (CNVs). A CNV can be: of no medical consequence; pathogenic resulting in physical and/or intellectual consequences; or protective against disease (e.g. HIV infection).

Reference DNA from control labeled Red

Test DNA from patient labeled Green

Glass microarray slide

Denature the DNA (separate the strands) and Hybridize to slide

Computer scans and analyzes signal outputs

Areas of loss (deletion)

Area of gain (duplication)

Who should be offered genetic testing?• Any child with autistic features should first be assessed by a

general or developmental pediatrican, and specialized autism testing used to provide a definitive diagnosis – Examples: Autism Diagnostic Observation Schedule [ADOS], Autism

Diagnostic Interview [ADI]

• If autism is confirmed, a genetics referral should be offered• The genetics assessment will look for unusual physical features

that might point to a syndrome or specific single gene disorder. These are most commonly found when the patient has “autism-plus” or complex ASD, with overgrowth, very large head, seizure disorder, muscle weakness or ataxia, cognitive regression, pigmentary abnormalities, or multiple congenital anomalies (25%)

• Initial work up:– 3 generation family history – Examination with special attention to dysmorphic features– Consider pediatric or genetic referral

• First tier genetic testing:– Chromosomal Microarray (CMA) to look for Copy Number Variants– Fragile X gene analysis– If evidence of regression, consider metabolic* workup

• Second tier genetic testing if first tier uninformative: – Genetic testing for specific single gene conditions– Possibly brain imaging

Who should be offered genetic testing?

Metabolic evaluation might include a complete blood count, ammonia, serum amino acids, urine organic acids and mucopolysaccharide testing. Specialist advice might be needed

What sorts of chromosomal microarray results might I receive?

• Normal – Excludes a microdeletion/microduplication (CNV) within the limits of resolution

of the test (typically very high) • Cannot completely rule out a CNV in all areas of the genome • Cannot exclude a syndrome caused by a mutation within a single gene• Cannot detect balanced chromosome differences

• Pathogenic microdeletion or microduplication (CNV)– CNV previously described and associated with a known phenotype, autism or

other

• Variation of unclear clinical significance (VUS)– Not every CNV in the genome is pathogenic– A variant that has not been described in the literature is challenging to interpret

and benefits from knowledge of parental status– Parental samples should be obtained and analysed – Next steps* before a referral to the Genetics clinic is initiated

VUS identified in child Test

parents

VUS identified in child Test

parents

Both parents have normal CMA results

Both parents have normal CMA results

One parent has same CMA result as child

One parent has same CMA result as child

• Finding in child is new, de novo

• Likely pathogenic

• Finding in child is new, de novo

• Likely pathogenic

• Finding in the child is normal familial variant

• Not pathogenic

• Finding in the child is normal familial variant

• Not pathogenic

• Finding in the child is pathogenic, but parent displays reduced penetrance (not everyone with the CNV will have symptoms), variable expressivity (individuals with this CNV have varied presentation)

• A second predisposing factor is needed to cause problems

• Finding in the child is pathogenic, but parent displays reduced penetrance (not everyone with the CNV will have symptoms), variable expressivity (individuals with this CNV have varied presentation)

• A second predisposing factor is needed to cause problems

What do these results mean for the recurrence risk of ASD?

• If no genetic cause is identified– Empirical studies suggest sibling recurrence risk (RR) is 10-18%

• If the sex of the next child is male his risk will be on the higher end

– If two siblings in one family are affected RR is 25-35%

• If a de novo pathogenic mutation/CNV is found– RR is 1% to account for rare gonadal mosaicism

• When a ASD ‘risk variant’ with incomplete penetrance and/or variable expressivity is identified– If de novo, RR of the CNV itself is <1%, but the empirical RR for ASD is

more difficult to predict. Empirical risks similar to simplex families– If inherited from a normal parent, RR is very difficult to decide as CNV

may not be the sole cause for the child’s ASD, however the CNV increased the ASD risk by indeterminate amount

How do I order the genetic test? • Genetic testing is generally performed on a blood sample• Specifics will depend on your region. Details can be found at

www.gecko-cegco.ca


• A specific diagnosis allows:– Better understanding of etiology, natural history and

prognosis– Informed treatment decisions– Specific anticipatory guidelines– Accurate recurrence risk information

• de novo pathogenic CNV versus ASD risk variant• Single gene disorder: disorder-specific risk depending on mode of

inheritance and whether de novo or not

– Prenatal diagnosis


• Previously addressed

Aidan•Floppy•Balance & coordination difficulties•Difficulty establishing sleep pattern•Hypersensitive to noise•Language delay

4 2

AliceA&W

BrettA&W

BeverlyA&W

BrendaA&W

BarbMenopause

at age 38

BenjaminA&W

CarlA&W

CathyA&W

CameronA&W

CoralA&W

AdamDevelopmental delay

1410 10

4244 34 36 26

555667 64

Key points• If autism is suspected

– refer for definitive diagnosis

• When autism or ASD is confirmed– Initial investigations– Refer to pediatrics or arrange first tier testing– Refer to genetics for dysmorphology examination and further testing

• Pearls: – The child with autism who has, in addition, overgrowth, a seizure disorder,

muscle weakness or ataxia, cognitive regression, pigmentary abnormalities, or multiple congenital anomalies is the one most likely to be diagnosed with a single gene disorder

– If the genetic cause of autism (spectrum) is diagnosed, family testing may be extremely important to establish risks for other relatives

References

• Carter M, Scherer SW. 2013. Autism spectrum disorder in the genetics clinic: a review. Clin Genet 83(5):399-407

• Schaefer GB, Mendelsohn NJ. 2013. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. Genet Med 15: 399-407.

• Flore LA, Milunsky JM. 2012. Updates in the genetic evaluation of the child with global developmental delay or intellectual disability. Semin Ped Neurol 19: 173-180.

Prenatal screening for genetic disorders:

Non-invasive prenatal testing

Genomics and Primary Care Seminar November 2013

Prenatal Screening tests for:DS, T18, T13 and ONTD

• Feb 2013

Around the same time

What is Non-invasive Prenatal Testing (NIPT)?

• Screening test to prenatally detect Down syndrome and other aneuploidies (extra or missing chromosomes)– trisomy 21, 18, 13– trisomy of sex chromosomes (XXX, XXY, XYY) – Turner syndrome (monosomy X)– triploidy (extra copy of all chromosomes)

NIPT• NIPT measures circulating cell free fetal DNA (ccffDNA)

present in maternal blood (from trophoblast)• Comprises ~10% of DNA in maternal blood• Increases with gestational age• ccffDNA analysis determines if normal, higher, or lower

than expected quantity of particular DNA sequences found on select chromosomes (13, 18, 21, X, Y)

• Performed on maternal blood sample• As early as 9 weeks’ gestation • Dating u/s – viability, accurate GA, exclude multiples

• 7 studies of “high risk” women • High risk:

– Screen positive– AMA (≥35 yrs)– Ultrasound findings– Family history indicating increased risk

• Previous pregnancy with aneuploidy

What’s the evidence for NIPT?


• By far most accurate performance for T21/18

Benn et al, Ultras Obstet Gynecol 2013, 42: 15-33


• 4 studies on unselected pregnancies– Most mixed risk, some after pos screen, AMA,

fewer with neg or no screen– > 14,000 pregnancies total, largest (11,000

significant loss to follow up)– Similar performance

• Not yet validated in low risk women, triplets or higher, pregnancies conceived with egg donation

Benn et al, Ultras Obstet Gynceol 2013, 42: 15-33


• Failed results– 6.1% (0.8-9.9) untested for insufficient sample

quality– 2% (436/22,222) no result after testing– Rarely happens with conventional screening– ccffDNA decreases with increased maternal BMI


Summary of evidence for NIPT


Disorder Sensitivity FPR

Down syndrome 99-100% ~0.1%

Trisomy 18 97-100% ~0.1%

Trisomy 13 79-92% ~0.1%

Sex chromosome differences

94-99%

Comparison of NIPT with other non-invasive prenatal screening tests

What do the experts say?

• American College of Obstetricians and Gynecologists 2012– Has been validated in industry sponsored studies

on at risk populations• History of prior pregnancy with trisomy• Positive multiple marker test • Parental balanced Robertsonian translocation with

increased risk of fetal trisomy 13/21• Maternal age >35• Fetal ultrasound findings with increased risk of

aneuploidy

ACOG Committee Opinion: Dec 2012


• Society of Obstetricians & Gynecologists of Canada 2013– Non-invasive prenatal testing using massive

parallel sequencing of cell-free fetal DNA to test for trisomies 21, 18, and 13 should be an option available to women at increased risk in lieu of amniocentesis. Pretest counselling of these women should include a discussion of the limitations of non-invasive prenatal testing.

Genetics Ctte Technical Update JOGC: Feb 2013


• Society of Obstetricians & Gynecologists of Canada 2013– No irrevocable obstetrical decision should be

made in pregnancies with a positive non-invasive prenatal testing result without confirmatory invasive diagnostic testing.

Genetics Ctte Technical Update JOGC: Feb 2013

Recommendation• Offer all women prenatal screening using either FTS,

IPS or MSS (SIPS or Quad)• IF screen +ve or at high risk for other reasons

– Consider NIPT as secondary screen of higher sensitivity if she is willing to pay for the test

• High risk:– Advanced maternal age– Previous aneuploidy pregnancy– Personal hx of sex chromosome aneuploidy (Turner

mosaic, XXX)– Abnormal u/s – Pregnancy conceived via reproductive technologies

Recommendation

• NIPT is not a replacement for diagnostic PN testing

• Positive NIPT should be confirmed by diagnostic testing: amnio or CVS

• Expected benefit of NIPT: fewer women having diagnostic tests with associated risk of pregnancy loss

Recommendation

• If result is negative → reassuring • NIPT cannot:

– Completely rule out aneuploidy– Detect chromosome differences other than

aneuploidy of chromosomes 13, 18, 21, X and Y– Detect single gene conditions– Detect congenital anomalies

• Still offer MSAFP and 18-20 wk ultrasound

Recommendation

• If result is positive: – Genetic counselling– Confirmation by diagnostic testing

No irrevocable obstetrical decisions should be made in pregnancies with abnormal NIPT results without confirmatory invasive testing (CVS or amnio) - SOGC

NIPT• Increasing demand from women (who can pay)• Increasing uptake in most (urban) centres• 3 separate companies, 3 separate technologies• No mechanism to evaluate centrally • Has it become mainstream now, become a

“standard of care”? (? Only for high risk women)• Heading for 2 tiered prenatal screening• Costs between $795 and $1200• 8-10 days for result

Where does NIPT fit with respect to the 11 to 14 wk scan?

• 11 to 14 week scan has value to pregnancy care– NT may shift in importance (importance to other

chromosomal, genetic and structural disorders)– Accurate dating/establishment of live fetus– Multiples/chorionicity affects management– Detects structural abnormalities

NIPT and counselling

• Likely primary providers will not have time/expertise to counsel in detail

• Refer to genetic counselling if your centre provides that service (significant impact on counselling demands)

• Company websites:– Panorama™ by Lifelabs– Harmony™ by Ariosa– Verifi™ by Verinata Health (Medcan)

Prenatal Screening Summary

• Offer all pregnant women, regardless of age, PN screening for fetal aneuploidy (trisomy 13, 18, 21) through FTS, IPS, SIPS or Quad screening

• + second trimester ultrasound for dating, assessment of fetal anatomy and detection of multiples

• Maternal age should not be used as a basis for recommending invasive testing when non-invasive PN screening is available

• Consider offering NIPT to high risk women or following a positive PN screen for aneuploidy

Prenatal Screening Summary

• Take a FH to identify familial and/or ethnically related disorders and screen accordingly

• Consider consanguinity and screen and test accordingly

• Refer or consult genetics when in doubt

Useful Genetics Resources• GEC-KO website: Genetics Education

www.gecko-cegco.ca• NIPT fact sheets:

– http://www.mountsinai.on.ca/care/family-medicine-genetics-program/prenatal

• Prenatal Screening Ontario Website– http://www.prenatalscreeningontario.ca/

Direct-to-consumer Genetic TestingDTC-GT


Case

• Jim, 53yo male • Healthy, active, non-smoker• Has been your patient for 15 years• Recently promoted as a corporate executive

and is being asked to undergo a thorough medical evaluation including personal genome testing and would like to know your thoughts

Family history

26

JimA&W

3A&W

JudyA&W

A&W

5453

42

A&W

A&W A&W

N

Prostate cancer

d.79 82

HypertensionArthritis

54Mid-50s

A&W

What is DTC-GT?• Direct-to-consumer genetic testing (DTC-GT)

– also referred to as personal genome testing– offered with the promise of providing:

• predictive genetic risk assessment for a variety of health conditions (i.e. diabetes, cancer, obesity)

• information about carrier status• information regarding response to and/or side-effect

risk of certain pharmaceuticals (i.e. clopidogrel, statins, antidepressants)

• Uses odds ratios and relative risks to categorize an individual as at increased risk (higher than average), average, or at decreased risk (lower than average)

• Can also screen for single gene disorders (e.g. cystic fibrosis, HFE-associated hemochromatosis, BRCA)

• Can uncover medically irrelevant information such as bitter taste perception or curly hair

What is DTC-GT?

What do I need to know about the genetics of DTC-GT?

• Uses data generated from genome-wide association studies (GWAS) – case-control studies which examine many common

variations in our genetic code (single nucleotide polymorphisms [SNPs])*

– compare large groups of individuals (unaffected controls versus individuals with symptoms of a specific disease) in an attempt to distinguish between non-harmful changes in the DNA code and pathogenic, disease-causing/predisposing changes

SNPs (pronounced ‘snips’) are the most common type of genetic variation. Each SNP represents a difference in a single DNA building block, a nucleotide. SNPs occur normally in an individual’s genome about once in every 300 nucleotides, and so there are about 10 million SNPs in the human genome

Who can obtain DTC-GT?

• Generally, DTC-GT is available online to anyone for a cost

• Genetic testing for DTC-GT is usually performed on a saliva sample


• While there are limited data to support the clinical validity (ability to predict clinical outcome) and utility (the likelihood of improving patient outcome), some consumers might benefit from DTC-GT as results may:– Encourage positive behaviour modifications (e.g. increase exercise,

smoking cessation) – Provide useful information for medication choice and/or dose, or

management – Provide information to individuals who have no or limited

information about their family history (e.g. an individual who was adopted)

– Reveal carrier status of a genetic condition that could have implications for family planning or medical management

Are there harms/limitations of DTC genetic testing?

• Caution when interpreting DTC-GT should be exercised as:– DTC-GT does not take into account numerous factors

important when interpreting genetic test results such as age, family history, lifestyle (e.g. smoking, obesity) and other environmental factors that are a significant contribution to common complex disease development

– Questionable clinical utility of some of reported results– Family health history-based risk assessment is still the

gold standard in the initial assessment for heritable conditions

• No testing regulation• Concerns re downstream testing and costs as result

of DTC results• “misattributed equivalence”

– if a DTC-GT test indicates a lower than average lifetime risk for a certain condition, when FH indicated a much higher risk, a consumer could be falsely reassured and not be as vigilant about medical interventions indicated by FH

– This phenomenon speaks to the need for knowledgeable healthcare provider involvement in pre- and post-test counselling

Are there harms/limitations of DTC genetic testing?

• Pearls– DTC-GT is over-the-counter genetic testing available online

to consumers through private companies– Generally, results report an individual’s probabilistic risk to

develop a medical condition based on genome wide association studies (GWAS)

– Results may provide medically useful information for consumers in addition to medically irrelevant information (e.g. curly hair)

– Interpret DTC results with caution– Family health history-based risk assessment is still the

gold standard in initial assessment for heritable conditions

References• Aiyar et al., 2013 Risk estimates for complex disorders: comparing

personal genome testing and family history. Genet Med. [Epub ahead of print]

• Goldsmith, L. et al., 2012. Direct-to-consumer genomic testing: systematic review of the literature on user perspectives. Eur J Hum Genet. 20:811-816

• Heald, B. et al., 2012. Prospective comparison of family medical history with personal genome screening for risk assessment of common cancers. Eur J Hum Genet. 20(5):547-51

• Special thanks to genetic counsellor Jill Davies at The Medcan Clinic

Faculty/Presenter Disclosure Faculty: Dr. June Carroll Program: 51 st Annual Scientific Assembly...

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