Frequently Asked Questions (FAQ) with our Lineagen Genetic Counselors

March 6, 2018
Deanna Leingang, MS, LCGC

Lineagen’s team of genetic counselors wear many hats as part of our clinical team. One of their favorite roles is acting as information resources for the patients and providers we serve. Here are some of the questions we receive most frequently from providers.

Ordering provider: “Is CMA appropriate for my patient?”
Genetic counselor: “Since chromosomal microarray analysis (CMA) is a broad test that can literally identify hundreds of different conditions with a broad range of symptoms and features, determining which patients are most likely to benefit from CMA can be a challenge for clinicians. Once upon a time, this type of testing was reserved for medical genetics clinics, who could offer highly trained clinical evaluation to determine the test or tests most likely to yield a diagnostic result. As technologies and our understanding of genetic disorders has expanded, genetic tests have moved into mainstream clinical care. Since individuals with autism spectrum disorders, developmental delays, or intellectual disability have a high risk of an underlying genetic disorder, the American Academy of Pediatrics (AAP), the American College of Medical Genetics (ACMG), and other professional societies have published guidelines recommending CMA, like Lineagen’s FirstStepDx PLUS, as a first tier diagnostic test for these individuals.
As genetics becomes a part of most branches of medicine, we’re here to help providers deliver the best information and care to their patients, both before and after testing. If you have questions about whether CMA is the most appropriate test for your patient based on their features or family history, our team is happy to help.”
Ordering provider: “What conditions does CMA detect?”
Genetic counselor: “CMA is a whole-genome test that detects missing or extra genetic information (deletions or duplications). While there are hundreds of disorders that can be identified with this testing, here are some of the most common conditions we see:
  • 15q11.2BP1-BP2 microdeletion, also called Burnside-Butler syndrome, is a condition that commonly presents with developmental and language delays and neuropsychiatric problems. While there can be some physical anomalies, like dysmorphic ears, palatal anomies, and brain abnormalities, this condition has incomplete penetrance and there is a great degree of variability in how significantly affected patients may be. Of note, most of the time this deletion is inherited from a parent who may or may not have any symptoms, so this result often has implications for multiple family members.
  • 22q11.2 deletion syndrome, which has been known by multiple names over the years, including DiGeorge and velocardiofacial syndrome, is a condition most providers have come across in school or practice. When this condition is diagnosed, a range of specialist evaluations and imaging studies may be indicated to detect and treat any previously undetected symptoms. This typically includes evaluation for palatal anomalies, like a submucosal cleft which may not be obvious, cardiology evaluation to detect and manage congenital heart defects, specialized evaluation and services for developmental delays, psychiatry evaluation due to increased risk for mental illnesses, and monitoring for hypocalcemia, immune dysfunction, and other health complications. Detailed guidelines for management of 22q11.2 deletion syndrome exist and can sometimes involve life-saving screening and procedures, making diagnosis important for both families and providers.
  • 16p11.2 deletion syndrome typically causes developmental delays, intellectual disability, and autism spectrum disorder. Some individuals may also experience epilepsy. While some may have minor physical abnormalities, there is not a specific set of features that are unique to this condition. 16p11.2 deletions are most often a new event (de novo), but cases of inherited deletions have been seen as well.
Ordering provider: “Will CMA detect NF1?”
Genetic counselor: “This is a common question amongst providers, because Neurofibromatosis type 1, or NF1, is a fairly common genetic disorder, affecting around 1 in 3000 people, and is frequently discussed in medical literature and may come up in a patient’s family history. This genetic condition characterized by pigmentation changes in the skin (cafĂ©-au-lait spots throughout the body and freckling along the groin and underarms) and the growth of tumors along nerves in the skin, brain, and other parts of the body (neurofibromas).
While some cases of NF1 are caused by deletions or duplications involved the NF1 gene, only about 5% of cases will be detected by CMA. The recommended approach to molecular diagnosis of this complex condition is a multi-step detection protocol that pairs genomic DNA sequence analysis, single gene deletion/duplication analysis, and cDNA analysis, which has around a 95% detection rate.
Most individuals with NF1 will have normal intelligence, but learning disabilities, behavioral problems, and autism spectrum disorder does occur in this condition at higher frequencies than in the general population. If your patient presents with delays or autism and NF1 is part of your differential, CMA may still be the best first tier test, since other chromosome abnormalities can cause these features. Be aware, however, that a normal result on CMA won’t be able to rule out NF1, and if you continue to suspect this condition, further testing or specialist evaluations may be needed.”

Ordering provider: “My patient has features of an autism spectrum disorder (ASD). Will CMA confirm whether my patient has autism?”
Genetic counselor: “This is a question that we frequently receive from both parents and providers. The purpose of CMA is to determine the underlying cause of features seen in a child. A positive result can provide a genetic diagnosis and potentially explain why the child is presenting with autistic features or developmental delays. However, CMA testing is not a substitute for clinical diagnostic evaluation, such as ADOS, to determine if a child has autism spectrum disorder (ASD).
Genetic testing is important because a genetic diagnosis in children with ASD can provide opportunities for anticipatory guidance, additional screenings, and services that they may not otherwise be aware of or be qualified for.”
These questions are just a small sample of the many provider inquiries our genetic counseling team receives each week. Our staff of 12 genetic counselors have a range of backgrounds in clinical and laboratory genetics across the country, and we enjoy sharing our passion for the power of genetic information with the doctors and patients that Lineagen serves. If you have a specific question or case you’d like to discuss with a Lineagen genetic counselor, please contact our clinical team by phone at 801-931-6191 or by email at