Common-Genetic-Tests-and-Indications-for-Testing

​Common Genetic Tests and Indications for Testing


COMMON GENETIC TESTS

Newborn Screening:

  • Testing performed in the first few days of a newborn's life to assess for disorders that might otherwise be missed due to the baby's normal appearance.
  • Tests are typically sent to the state's newborn screening lab for assessment.
  • Includes hearing a critical heart screening.
  • All states require newborn screening for at least 26 conditions.
    • Some states require screening for up to 50 conditions.
  • There are 5 main categories screened for in newborn screening
    • Organic acid metabolism disorders
    • Fatty acid oxidation disorders
    • Amino acid metabolism problems
    • Hemoglobin problems
    • Other (which includes such things as congenital hearing loss, critical heart problems, cystic fibrosis, galactosemia, and congenital hypothyroidism
  • The Newborn Screening page from the Centers for Disease Control and Prevention provides a number of resources on newborn screening including a variety of multimedia tools, links to programs, and additional materials.
  • What is Newborn Screening?
    This page from the Association of Public Health Laboratories provides general newborn screening information, parental considerations, and information on state newborn screening programs.
  • Implications of newborn screening for nurses
    Published: Journal of Nursing Scholarship, March 2013
    Authors: DeLuca J, Zanni KL, Bonhomme N, and Kemper AR
  • Newborn Screening ACT Sheets and Confirmatory Algorithms

Prenatal Screening:

  • Testing performed during pregnancy to determine the risk of possible health issues such as a chromosomal abnormality or birth defect in the developing child.
  • Prenatal genetic screening is not required and not all health problems can be detected before delivery.
  • Examples of prenatal screening and tests include:
    • Ultrasound
    • Maternal Blood Tests
    • Amniocentesis
    • Chorionic Villus Sampling
  • A new era in noninvasive prenatal testing
    Published:The New England Journal of Medicine, July 2013
    Authors: S Morain, MF Greene, and MM Mello
  • Best ethical practices for clinicians and laboratories in the provision of non-invasive prenatal testing
    Published: The Journal of the American Medical Association, April 2013
    Authors: Christopher G Chute and Isaac S Kohane
  • ACMG position statement on prenatal/preconception expanded carrier screening
    Published: Genetics in Medicine, April 2013
    Authors: Wayne W Grody, Barry H Thompson, Anthony R Gregg, Lora H Bean, Kristin G Monaghan, Adele Schneider, Roger V Lebo
  • Point of Care Fact Sheets for the Prenatal Provider
    These fact sheets from the National Coalition for Health Professional Education in Genetics were developed with the aim of providing information about genetic and family history risks that may be identified in patients. The fact sheets contain background information, next steps for evaluation, and the relevant clinical guidelines.
  • The Pregnancy & Health Profile: A Risk Assessment & Screening Tool
    This user-friendly, tablet-based tool assists providers and patients in identifying risk based on family history information, and informs shared decisions on prenatal testing and screening. Available for download through the National Coalition for Health Professional Education in Genetics, this tool was designed to replace paper forms and to streamline the patient intake process.

Karyotype:

  • Test to identify and evaluate the size, shape, and number of chromosomes in a sample of body cells.
  • Can be used to identify trisomies, sex chromosomal anomalies, visible deletions/duplications, and translocations.
  • Not effective at clearly defining breakpoints in a chromosome with specific delineated gene impact.
  • Examples of use include:
    • Determining whether the chromosomes of an adult have an abnormality that can be passed to offspring
    • Determining whether a chromosome defect is preventing pregnancy or is causing miscarriages
    • Determining whether a chromosome defect is present in a fetus
    • Determining the cause of a birth defect of disability

DNA Microarray:

  • Microarray technology is used to study the expression of many genes at once.
  • Involves placing thousands of gene sequences in known locations on a glass slide called a gene chip. A sample containing DNA or RNA is placed in contact with the gene chip. Complementary base pairing between the sample and the gene sequences on the chip produces light that is measured. The areas on the chip producing light identify genes expressed in the sample. (Source: Genetics Home Reference)
  • Useful for detecting microdeletions/microduplications and specific breakpoints of genes impacted from an unbalanced translocation.
  • Commonly used to identify etiologies of patients with multiple congenital anomalies, autism, or developmental delay.
  • Does not detect specific gene mutations, only missing or duplicated genes.
  • Clinical Utility of Chromosomal Microarray Analysis
    Published: Pediatrics, October 2012
    Authors: JW Ellison, JB Ravnan, JA Rosenfeld, SA Morton, NJ Neill, MS Williams, J Lewis, BS Torchia, C Walker, RN Traylor, K Moles, E Miller, J Lantz, C Valentin, SL Minier, K Leiser, BR Powell, TM Wilks, and LG Shaffer
  • Array-Based Technology and Recommendation for Utilization in Medical Genetics Practice for Detection of Chromosomal Abnormalities
    Published: Genetics in Medicine, November 2010
    Authors: M Manning, L Hudgins; Professional Practice and Guidelines Committee
  • Chromosomal Microarray Testing Influences Medical Management
    Published: Genetics in Medicine, September 2011
    Authors: ME Coulter, DT Miller, DJ Harris, P Hawley, J Picker, AE Roberts, MM Sobeih, M Irons

Whole Genome/Exome Sequencing:

  • Whole exome sequencing allows for variations in the protein-coding region of any gene to be identified.
  • The current limitation of this process is the expense, but this is expected to change as technologies advance
  • While many more genetic changes can be identified than with select gene sequencing the significance of much of this information is unknown. It is difficult to know whether identified variants are involved in the condition of interest.
  • Practices and Policies of Clinical Exome Sequencing Providers: Analysis and Implications
    Published: American Journal of Medical Genetics Part A, May 2013
    Authors: SM Jamal, J Yu, JX Chong, KM Dent, JH Conta, HK Tabor, and MJ Bamshad
  • Implementing Genomic Medicine in the Clinic: The Future is Here
    Published: Genetics in Medicine, January 2013
    Authors: TA Manolio, RL Chrisholm, B Ozenberger, DM Roden, MS Williams, R Wilson, D Bick, EP Bottinger, MH Brilliant, C Eng, KA Frazer, B Korf, DH Ledbetter, JR Lupski, C Marsh, D Mrazek, MF Murray, PH O'Donnel, DJ Rader, MV Relling, AR Shuldiner, D Valle, R Weinshilboum, ED Green, and GS Ginsburg
  • Clinical Application of Exome Sequencing in Undiagnosed Genetic Conditions
    Published: Journal of Medical Genetics, May 2012
    Authors: AC Need, V Shashi, Y Hitomi, K Schoch, KV Shianna, MT McDonald, MH Meisler, and DB Goldstein

FISH Analysis:

  • Fluorescence in situ hybridization (FISH) is a laboratory technique for detecting and locating a specific DNA sequence on a chromosome.
  • Relies on exposing chromosomes to a DNA probe containing a fluorescent molecule attached to it, which then binds to its corresponding sequence on the chromosome.
  • Commonly used to detect trisomies, sex chromosome anomalies, and specific syndromic deletions such as 22q11 deletion (DiGeorge syndrome) and William's syndrome.



KEY CONSIDERATIONS FOR GENETIC TESTING

The role of the primary care provider (PCP) related to genetic medicine is changing. The first step in ordering a genetic test is increasingly likely to fall on the PCP. When considering ordering a genetic test in a primary care setting, the provider is encouraged to consider the following three steps.

  1. Identify reasons for genetic testing (autism, delays, congenital anomalies, family history of a particular disorder, etc.)
  2. Identify individuals in the family to be tested
  3. When should I refer my patient for genetics consultation?



 

Identify Reasons for Testing Identifying Family Members to Test
  • Affected family member
    • Testing is most informative when testing starts with an affected family member
  • At-risk relatives
  • Key question = why does my patient need genetic testing?
  • Consider consultation with a genetics professional
Considerations for Genetics Consultation
  • A personal or family history of a genetic condition, birth defect, chromosomal disorder, or hereditary cancer
  • Two or more miscarriages
  • A known inherited disorder, birth defect, mental retardation, or developmental delay in a child
  • A woman who is pregnant or plans to become pregnany at or after age 35
  • Abnormal test results suggesting a potential genetic or chromosomal condition
  • An increased risk of developing or passing on a particular genetic disorder on the basis of the individual's ethnic background
  • A consanguineous couple planning to have a child together

LABORATORY TESTING

What is biochemical genetic testing?
Biochemical genetic testing involves the study of enzymes in the body. These enzymes could be deficient or absent, have altered activity, or be unstable which can lead to clinical manifestations in an affected person.

These types of disorders are known as "inborn errors of metabolism" since they are present from birth and directly impact the body’s metabolism.

There are hundreds of enzyme defects that are well defined in humans. From a laboratory standpoint, we can study the enzyme itself (which is the product of the gene) to assess its functioning. The approach depends on the disorder.

Sometimes, the gene mutations responsible for inborn errors of metabolism are not fully elucidated at today’s level of genomic knowledge and expertise. Thus, checking for a specific gene mutation is not always a good solution. Additionally, biochemical tests are ideal for screening less expensively for inborn errors of metabolism than gene specific analysis.

Biochemical genetic studies may be done from a urine or blood sample, spinal fluid, or other tissue sample. Various labs across the country specialize in this type of testing.

Common disorders associated with inborn errors of metabolism include:

  • Phenylketonuria
  • Galactosemia
  • Biotinidase deficiency
  • Hereditary hemochromatosis

Common types of biochemical testing are as follows:

  • Urine organic acids,
  • Serum amino acids,
  • Ammonia level,
  • Acylcarnitine profile, and
  • Creatine kinase

*These tests are commonly utilized as screening or diagnostic tools. Many times geneticists/pediatricians will begin with these as a general measure, then move on to more specific biochemical genetic testing depending on the symptomatology.

Additional testing could include:

  • 7,8-dehydrocholesterol for cholesterol biosynthesis disorders
  • Acylcarnitine profile for fatty acid oxidation defects
  • Glycosylation status of transferrin for congenital disorders of glycosylation
  • Fatty acid profile for fatty acid oxidation defects
  • Urine oligosaccharides for oligosaccharidoses
  • Urine mucopolysaccharides for mucopolysaccharidoses
  • White blood cell enzyme screen analysis for lysosomal storage disorders
  • Very long chain fatty acid analysis/phytanic acid analysis for peroxisomal disorders
  • Total homocysteine and serum methionine for homocystinurias
  • Urine S-sulfocysteine
  • Urine succinylpurines
  • Serum uric acid
  • Urine creatine/guanidinoacetate
  • Urine succinylacetone for tyrosinemia
  • Lactate and pyruvate (serum or CSF)
  • Urine orotic acid
  • Plasmalogens for peroxisomal disorders
  • Quantitative glutaric acid and 3-OH glutaric acid levels
  • Carnitine panel

 

PHARMACOGENOMIC TESTING

Pharmacogenomics is the study of many genes that determine the behavior of drugs on the body.

Pharmacogenetics refers to the study of inherited variations in genes responsible for drug response and the science to determine how a patient will respond to certain medications—positively, negatively, or no response.

Many drugs that are currently available are "one size fits all," but they do not work the same way for everyone. It can be difficult to predict who will benefit from a medication, who will not respond at all, and who will experience an adverse reaction. Research is being done to determine how to utilize an individual's genetic differences to predict their response to and the effectiveness of a medication, and prevent adverse drug reactions.

In the future, pharmacogenomics will allow the development of tailored drugs to treat a wide range of health problems, including cardiovascular disease, Alzheimer disease, cancer, HIV/AIDS, and asthma.

Where can I learn more about pharmacogenomics in primary care?
The National Institute of General Medical Sciences offers a list of Frequently Asked Questions about Pharmacogenomics.

The National Center for Biotechnology Information provides a discussion of this topic as part of its Science Primer: One Size Does Not Fit All: The Promise of Pharmacogenomics.

Pharmacogenomic testing: Relevance in medical practice: Why drugs work in some patients but not in others
Published: Cleveland Clinic Journal of Medicine, April 2011
Authors: Joseph P Kitzmiller, MD, PhD, David K Groen, MD, Mitch A Phelps, PhD, and Wolfgang Sadee, Dr rer nat

Pharmacogenomics for the primary care provider: Why should we care?
Published: Cleveland Clinic Journal of Medicine, April 2011
Author: Kathryn Teng, MD

PharmGenEd™
From the University of California San Diego Skaags School of Pharmacy and Pharmaceutical Science, this CME-bearing, two module program aims to increase awareness about the validity and utility of pharmacogenomic tests.

ADDITIONAL RESOURCES

Ordering the Right Tests Time Out for Genetics webinar

New Guidelines on Genetic Testing and Screening in Children
Published: AAP Grand Rounds, September 2013
Author: R Hamid
This article provides a summary of the major recommendations for genetic testing in children recently released from the American Academy of Pediatrics and the American College of Medical Genetics and Genomics.

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