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6B Congenital Anomalies

Description | Specific Indicators | Ontario Public Health Standards | Corresponding Health Indicator(s) from Statistics Canada and CIHICorresponding Indicator(s) from Other Sources | Data Sources |  Alternative Data Sources | Analysis Check List | Method of Calculation |  Basic Categories | Indicator Comments | Definitions | Cross-References to Other Indicators | Cited References  | Other References | Changes Made | Acknowledgements 


  • The rate of congenital anomalies is the number of births (live births and stillbirths) identified as having a given congenital anomaly, expressed as a percentage of the total number of births (live births and stillbirths).
Specific Indicators
  • Rate of congenital anomalies (CAs)
  • Rate of neural tube defects (NTDs)
  • Rate of Down syndrome (DS)
  • Rate of congenital heart defects (CHDs)
  • Rate of orofacial clefts (OFCs)
  • Rate of musculoskeletal anomalies (MSKs)
Ontario Public Health Standards (OPHS)
The Ontario Public Health Standards (OPHS) establish requirements for the fundamental public health programs and services carried out by boards of health, which include assessment and surveillance, health promotion and policy development, disease and injury prevention, and health protection. The OPHS consist of one Foundational Standard and 13 Program Standards that articulate broad societal goals that result from the activities undertaken by boards of health and many others, including community partners, non-governmental organizations, and governmental bodies. These results have been expressed in terms of two levels of outcomes: societal outcomes and board of health outcomes. Societal outcomes entail changes in health status, organizations, systems, norms, policies, environments, and practices and result from the work of many sectors of society, including boards of health, for the improvement of the overall health of the population. Board of health outcomes are the results of endeavours by boards of health and often focus on changes in awareness, knowledge, attitudes, skills, practices, environments, and policies. Boards of health are accountable for these outcomes. The standards also outline the requirements that boards of health must implement to achieve the stated results.

Outcomes Related to this Indicator 
  • Board of Health Outcome (Reproductive Health): The board of health is aware of and uses epidemiology to influence the development of healthy public policy and its programs and services for the promotion of reproductive health.
  • Board of Health Outcome (Foundational Standard): The public, community partners, and health care providers are aware of relevant and current population health information Assessment and/or Surveillance Requirements Related to this Indicator.
Assessment and Surveillance Requirements Related to this Indicator (Reproductive Health)
  • The board of health shall conduct epidemiological analysis of surveillance data... in the area of reproductive health outcomes. 

Corresponding Health Indicator(s) from Statistics Canada and CIHI

  • None
Corresponding Indicator(s) from Other Sources  
  • Canadian Perinatal Surveillance System: Neural Tube Defect Rate; Prevalence of Congenital Anomalies
Data Sources (see Resources: Data Sources)  

Numerator & Denominator: Canadian Congenital Anomalies Surveillance System (CCASS)

Original source: Canadian Institute for Health Information (CIHI)
Distributed by: Public Health Agency of Canada 
Suggested citation (see Data Citation Notes): CCASS [years], Public Health Agency of Canada, Date Extracted: [date]

Alternative Data Sources  

Numerator & Denominator: BORN Information System

Original source: Better Outcomes Registry Network (BORN) Ontario
Distributed by: Better Outcomes Registry Network (BORN) Ontario
Suggested citation (see Data Citation Notes):  BORN Information System [years], Date Extracted: [date].


Analysis Check List  
  • Aggregated data of counts, rates and confidence intervals from CCASS are provided by the Public Health Agency of Canada.
  • Refer to the Canadian Congenital Anomalies Surveillance System (CCASS) Data Source for more information about the data.
  • HELPS Data: Historically, PHUs obtained data for live births, stillbirths, therapeutic abortions, congenital anomalies, and deaths from the Ministry of Health through HELPS (the HEalthPlanning System). Although these data are no longer commonly used, some PHUs may still be accessing these data files. Information about the data can be found in the HELPS Data Source resource.
Method of Calculation 
Rate of Congenital Anomalies

total number of live births or stillbirths identified as having at least one congenital anomaly

x 10,000

total number of births (live births & stillbirths)

Rate of Neural Tube Defects

total number of live births or stillbirths identified with a neural tube defect

x 10,000

total number of births (live births & stillbirths)


Down Syndrome

total number of live births or stillbirths identified with Down syndrome

x 10,000

total number of births (live births & stillbirths)


Orofacial Clefts

total number of live births or stillbirths identified with orofacial clefts

x 10,000

total number of births (live births & stillbirths)


Musculoskeletal Anomalies

total number of live births or stillbirths identified with musculoskeletal anomalies

x 10,000

total number of births (live births & stillbirths)


Congenital Heart Defects

total number of live births or stillbirths identified with congenital heart defects 

x 10,000

total number of births (live births & stillbirths)


Basic Categories  
  • Geographic area of residence: Ontario, census division, census sub-division. Public health unit is not available in CCASS data but most PHUs correspond to a census division or groupings of census divisions. Refer to CCASS Data Source resource for further details.
Indicator Comments  
  • Congenital anomalies, also called birth defects or congenital malformations, are a leading cause of infant death, particularly in the postneonatal period (age 28 to 364 days). In 2004, congenital anomalies was the second most common cause of infant death after immaturity, representing 23.6 per cent of all infant deaths in Canada (excluding Ontario) (1).
  • Some congenital anomalies may be under-reported due to no diagnosis of the condition at birth and no hospitalization with the condition identified prior to 28 days; or termination of the pregnancy due to screening for these conditions. Under-reporting may vary over place and time and by type of anomaly. Therapeutic terminations performed due to screening are not currently captured in CCASS but are part of the new BORN Information System and will be incorporated in CCASS starting in 2012.
  • Technologic changes with respect to prenatal screening in the last two decades have resulted in increased uptake of prenatal diagnosis and pregnancy termination for serious congenital anomalies. As a result, the birth prevalence and infant mortality of some anomalies has decreased while stillbirth rates and neonatal death rates due to congenital anomalies or pregnancy termination have increased. From the mid-1990s onwards, stillbirths among fetuses <500 g have been increasingly coded with cause of death as pregnancy termination rather than congenital anomaly (2, 3).
  • Most congenital anomalies (40%-60%) are from unknown causes. General causes include recognized genetic conditions and environmental factors such as maternal obesity, insulin-dependent diabetes, infections, and drug and chemical exposures. Most congenital anomalies causes are believed to be multi-factorial whereby both environmental and genetic factors are involved (4).
  • Maternal obesity has been identified as a risk factor for a variety of congenital anomalies, particularly neural tube defects. The mechanism is unclear but may relate to nutrition, glycemic control and diabetes, genetics or other biological effects. As well, the prenatal detection of anomalies may be less effective in obese women, potentially resulting in fewer terminations and a higher birth prevalence of infants with congenital anomalies (5).
       Neural Tube Defects:
  • Neural tube defects (NTDs) occur when the tube that forms the spinal cord and brain fails to close during the third and fourth week of pregnancy. NTDs primarily include anencephalus, spina bifida and encephalocele. Some infants may have more than one of these conditions. The total number of cases of NTDs should be used rather than the sum of each type of NTD to avoid double-counting.
  • The rate of NTDs may be affected over time and place due to the availability of genetic screening and resultant therapeutic termination, and the use of folic acid supplementation.
  • In 1998, the Government of Canada mandated the fortification of all white flour and pasta products. This policy change was expected to add approximately 100 micrograms of folic acid daily to the average Canadian's diet (6).
  • Some evidence has demonstrated that rates of NTDs such as spina bifida have decreased overall in Canada (7). The overall prevalence of neural-tube defects at birth in seven Canadian provinces (Ontario excluded) decreased from 1.58 per 1,000 births before the fortification mandate, to 0.86 per 1,000 births during the full-fortification period, a 46% reduction (8). Although folic acid supplementation has been shown to reduce the rate of neural tube defects, it does not eliminate them altogether (9).
       Down Syndrome:
  • Down syndrome (DS), also known as Trisomy 21, is one of the most common and widely recognized congenital anomalies (4).
  • The only well established risk factor for DS is advancing maternal age. The probability of DS in a 20 year old woman is approximately 1 in 1000, compared to 1 in 60 in a 40 year old (10). Age 35 is typically considered the cut-off point delineating significantly increased risk for DS.
  • With average maternal age in Canada and many other industrialized countries increasing, overall DS rates are increasing (11, 12). Some research shows elective pregnancy terminations following prenatal diagnosis of DS are increasing, particularly in older women (11-13). As a result, the true birth prevalence of DS may be stable or decreasing, despite more births among older mothers.
       Congenital Heart Defects: 
  • Congenital Heart Defects (CHDs) are among the most common congenital disorders and are the leading cause of infant death due to congenital anomalies (14).
  • Most cases of CHDs are born to couples with no prior family history or maternal risk factors (4).
  • Adequate folic acid intake may reduce the risk of CHDs, in addition to NTDs. Fortification of foods with folate in Canada was shown to reduce rates of CAs other than NTDs, such as CHDs (15).
  • Maternal diabetes mellitus and phenylketonuria increase the risk of certain types of CHDs (15-17).
       Oral Facial Clefts: 
  • Oral facial clefts (OFCs) include two genetically distinct anomalies - cleft palate (CP), and cleft lip with or without cleft palate (CL/P). In Canada, the distribution of cleft types for live births from 2002/03 to 2007/08 was 17% CL, 41% CP and 42% CLP (18). OFCs often occur in association with other major anomalies (4).
  • There is no identifiable environmental cause in the majority of OFC cases. A number of drugs and environmental agents have been implicated but studies are often inconsistent. Maternal smoking during pregnancy has been consistently associated with increased risk. Maternal use of multivitamin supplements in early pregnancy is generally associated with a reduced risk of OFC, but studies of an association with folic acid are inconsistent (9, 19, 20).
  • OFCs can be detected prenatally through ultrasound. Although cases with isolated OFCs would be unlikely to be terminated, detected cases that occur in conjunction with other major anomalies may result in pregnancy termination (4).
       Musculoskeletal Anomalies:
  • Musculoskeletal (MSK) anomalies are physically classified as either limb or axial, and may be localized, as in a single club foot, or generalized, as in osteogenesis imperfecta (21).
  • MSK anomalies are the most prevalent anomalies in Ontario (22).
  • Ultrasonography is the most popular prenatal detection method for MSKs; however, many MSKs are not confirmed in the prenatal period. Many MSK anomalies are only detectable postnatally, requiring postnatal examination for accurate diagnosis and prediction of recurrence (23).
  • With the exception of the thalidomide tragedy (1950-1960), relatively few limb reductions can be conclusively attributable to teratogenic agents (24).
  • Congenital anomaly - a condition that results from an abnormality of structure, function or metabolism in one or more parts of the body, with potential to adversely affect health, development or function. Anomalies are present at birth and may be inherited genetically, acquired during gestation, or inflicted during birth. Also called a birth defect.
  • Live birth - the complete expulsion or extraction from its mother of a product of conception, irrespective of the duration of the pregnancy, which, after such separation, breathes or shows any other evidence of life such as heartbeat, umbilical cord pulsation, or definite movement of voluntary muscles, whether the umbilical cord has been cut or the placenta is attached. A live birth is not necessarily a viable birth.
  • Stillbirth - death prior to the complete expulsion or extraction from its mother of a product of conception. The death is indicated by the fact that after such separation the fetus does not breathe or show any other evidence of life, such as beating of the heart, pulsation of the umbilical cord, or definite movement of voluntary muscles. Only fetal deaths where the product of conception has a birth weight of 500 grams or more or the duration of pregnancy is 20 weeks or longer are registered in Canada.
  • Neural tube defect - a genetic malformation involving the skull and spinal cord. These defects are primarily caused by a failure of the neural tube to close during development of the embryo. Diagnostic tests (maternal serum screening, amniocentesis, and ultrasound) are available but not 100% sensitive or specific. Neural tube defects include: anencephalus, spina bifida, and encephalocele.
  • Down syndrome - a congenital anomaly that occurs as a result of an error in the production of the egg (or less commonly in the sperm) or in early mitosis following conception. Normally cells contain 21 pairs of chromosomes; in DS, there is a third copy of the 21st chromosome present (8).
  • Congenital heart defects - a group of congenital anomalies involving genetic malformation of the structure of the heart or great vessels which is present at birth.
  • Orofacial clefts - anomalies of the lip and palate that develop during the critical period of development of the lip and primary palate (five to seven weeks following conception) and the secondary palate (eight to twelve weeks following conception) (8).
  • Musculoskeletal anomalies - are disorders of the musculoskeltal system present at birth. They can be due to deformity or malformation (20). Musculoskeletal anomalies include: limb reductions, congenital dislocation of the hip, clubfoot, polydactyly, macrocephaly, congenital scoliosis, and spina bifida occulta.
Cross-References to Other Indicators
  • None 
Cited References  
  1. Lindsay J, Dzakpasu S, Allen A. Infant Mortality Rate. In: Canadian Perinatal Health Report, 2008 Edition. Public Health Agency of Canada. Ottawa, 2008. Available from: Accessed on March 9, 2012.
  2. Public Health Agency of Canada. An Overview of Perinatal Health in Canada. In: Canadian Perinatal Health Report, 2008 Edition. Ottawa, 2008. Available from: Accessed on March 9, 2012.
  3. León JA, Evans J, Royle C. Prevalence of Congenital Anomalies. In: Canadian Perinatal Health Report, 2008 Edition. Public Health Agency of Canada. Ottawa, 2008. Available from: Accessed on March 9, 2012.
  4. Health Canada. Congenital Anomalies in Canada: A perinatal health report, 2002. Ottawa: Minister of Public Works and Government Services Canada, 2002. Available from: on September 5, 2012.
  5. Carmichael SL, Rasmussen SA, Shaw GM. Prepregnancy obesity: A complex risk factor for selected birth defects. Birth Defects Research Part A: Clinical and Molecular Teratology. 2010; 88: 804-810.
  6. Government of Canada. Regulatory impact analysis statement SOR/98-550. Canada Gazette. 2003; (132):3029-4.
  7. De Wals P, Tairou F, Van Allen MI, Lowry RB, Evans JA, Van den Hof MC, et al. Spina bifida before and after folic acid fortification in Canada. Birth Defects Res A Clin Mol Teratol. 2008; 82(9):622-6.
  8. De Wals P, Tairou f, Van Allen MI, Uh SH, Lowry RB et al. Reduction in Neural-Tube Defects after Folic Acid Fortification in Canada. N Engl J Med. 2007; 357:135-42.
  9. Heseker HB, Mason JB, Selhub J, Rosenberg IH, Jacques PF. Not all cases of neural-tube defect can be prevented by increasing the intake of folic acid. Br J Nutr. 2009, 102; 173-180.
  10. Marttala J, Yliniemi O, Gissler M, Nieminen P, Ryynanen  M. Prevalence of Down's syndrome in a pregnant population in Finland. Acta Obstetricia Et Gynecologica Scandinavica. 2010; 89(5), 715-717.
  11. Morris JK, Alberman E. Trends in Down's syndrome live births and antenatal diagnoses in England and Wales from 1989 to 2008: Analysis of data from the National Down Syndrome Cytogenetic Register. BMJ (Clinical Research Ed.). 2009; 339: b3794.
  12. Cocchi G, Gualdi S, Bower C, Halliday J, Jonsson B, Myrelid A, Annerén G. International trends of Down syndrome 1993-2004: Births in relation to maternal age and terminations of pregnancies. Birth Defects Research Part A. Clinical and Molecular Teratology. 2010; 88(6): 474-479.
  13. Siffel C, Correa A, Cragan J, Alverson CJ. Prenatal diagnosis, pregnancy terminations and prevalence of Down syndrome in Atlanta. Birth Defects Research.Part A. Clinical and Molecular Teratology. 2004; 70(9):565-571.
  14. Agha MM, Glazier R H, Moineddin R, Moore AM, Guttmann A. Socioeconomic status and prevalence of congenital heart defects: Does universal access to health care system eliminate the gap? Birth Defects Research Part A. Clinical and Molecular Teratology. 2011; 91(12):1011-18.
  15. Ionescu-Ittu R, Marelli A J,  Mackie A S,  Pilote L. Prevalence of severe congenital heart disease after folic acid fortification of grain products: time trend analysis in Quebec, Canada. BMJ (Clinical Research Ed.). 2009; 338: b1673.
  16. van der Bom T, Zomer AC, Zwinderman A H, Meijboom  FJ, Bouma  BJ, Mulder BJ. The changing epidemiology of congenital heart disease. Nature Reviews.Cardiology. 2011: 8(1), 50-60.
  17. Lisowski LA, Verheijen PM, Copel JA, Kleinman CS, Wassink S, Visser GH, Meijboom, EJ. Congenital heart disease in pregnancies complicated by maternal diabetes mellitus: an international clinical collaboration, literature review, and meta-analysis. Herz. 2010: 35(1), 19-26.
  18. Pavri S, Forrest CR. Demographics of Orofacial Clefts in Canada from 2002 to 2008. Cleft Palate Craniofacial J. 2011 Sep 9.
  19. Ray JG, Meier C, Vermeulen MJ, Wyatt PR, Cole DE. Association between folic acid food fortification and congenital orofacial clefts. J. Pediatr. 2003; 143(6):805-7.
  20. Little, J. Overview of epidemiology and aetiology of orofacial clefts. Current Topics: Canadian Congenital Anomalies Surveillance Network. Available from: Accessed: March 8, 2012.
  21. Salter RB. Textbook of Disorders and Injuries of the Musculoskeletal System. 1999 Edition. Maryland: Lippincott Williams & Wilkins, 1999.
  22. Public Health Agency of Canada. Unpublished tables from the Canadian Congenital Anomalies Surveillance System, 2009.
  23. Khalil  A, Pajkrt E, Chitty LS. Early prenatal diagnosis of skeletal anomalies. Prenat Diagn. 2011; 31(1):115-24.
  24. Sanders DD, Stephens TD. Review of drug-induced limb defects in mammals. Teratology. 1991; 44: 335-54.
Other References
Changes Made


Type of Review - Formal or Ad Hoc

Changes Made By

Changes Made

March 2010


Reproductive Health Sub-Group

  • Replaced Mandatory Health Programs section with updated Ontario Public Health Standards outcomes.

March 30, 2012 - January 16, 2013


Reproductive Health Sub-Group

  • Changed indicator from Neural Tube Defects to Congenital Anomalies, adding total CA rate as a specific indicator along with the following: Neural tube defects, Down syndrome, orofacial clefts, musculoskeletal anomalies, congenital heart defects.
  • Updated CCASS Data Source
 January 14, 2014 Ad hoc Mary-Anne Pietrusiak

 Added Congenital Anomalies in Canada 2013 report under Other References




Lead Authors

  • Jessica Deming, Region of Waterloo Public Health
  • Mary-Anne Pietrusiak, Durham Region Health Department
  • Sherrie Kelly, BORN Ontario

Contributing Authors

  • Reproductive Health Sub-Group


  • Sarah Collier, Toronto Public Health
  • Jocelyn Rouleau, Public Health Agency of Canada
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