Genetic testing, providing answers for two daughters

It was a typical day in the summer. I (Anum Shafique) went to locate families with epileptic disorders in the outpatient department of a hospital in Lahore. A family with two children was visiting at the same time seeking help. The mother was worried about her two daughters that were suffering from seizures. Every month, she had to visit the doctor to adjust the dosage of medicine they were prescribed for treating the seizures. However, the seizures did not improve. The mother was also having a hard time traveling to the hospital because one of the daughters also suffered from intellectual disability along with epilepsy. The mother said that her daughter was fine at birth but suffered brain damage as a result of the seizures. The two daughters’ epilepsy type was not responsive to medication, so the neurologist was curious about its causes. Afterward, I talked to the patients’ mother and asked for her consent to further investigate her daughters’ cases.

Two children with sezures. One of them had intellectual disability as symptom due to seizure-induced brain damage.

The mother informed me that the daughters had multiple seizure episodes per day. Since I was looking for information in her own words, I also asked for the daughters’ medical histories again. Having gathered the necessary clinical information, I met with the neurologist. We discussed and found that certain types of epilepsies require specific medications. The probability that genetic factors were involved was high since the parents of the two affected girls were consanguineous and unaffected. In order to save time and money, I recommended the patients’ family to provide samples to undergo exome sequencing, so that I can look more closely into the more than 20,000 genes an exome analyzes.

My supervisor, Professor Sadaf Naz, then contacted 3billion's laboratory in South Korea, with whom she had a collaborative project. DNA of both sisters was processed by the company and results were obtained within a month after processing the samples.

Discovering a simple treatment to an unsolvable mystery

Mechanism of ALDH7A1 gene variant causing reduced activity of pyridoxine

I was glad to find the answer to the treatment-resistant mystery the two daughters were suffering from when the results appeared on the 3billion online portal. In light of all clinical and genetic findings, it was determined that the sisters suffered from pyridoxine-dependent epilepsy due to a variant in the ALDH7A1 gene. Sanger sequencing was used to confirm the segregation of this gene variant. As expected, this variant was heterozygous in both unaffected parents. Thankfully, the unaffected brother had only the wild-type alleles, and the other unaffected sister was a heterozygous carrier. As expected, both patients were homozygous for the variant in ALDH7A1 as had been determined by exome sequencing.

Variants of ALDH7A1 cause Pyridoxine-dependent epilepsy (OMIM #266100). This gene provides instructions for making an enzyme, also known as antiquitin, which is involved in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. It is also involved in the catabolism of lysine in the mitochondria. Variants that cause pyridoxine-dependent epilepsy produce nonfunctional antiquitin proteins or result in loss of protein. Antiquitin deficiency leads to an accumulation of α- aminoadipic semialdehyde, reducing the activity of pyridoxine, a form of vitamin B6 derived from food. There are many processes in the body that require pyridoxine, such as for breakdown of amino acids and the production of neurotransmitters in the brain. It is not clear how the seizures associated with this condition are caused by a lack of pyridoxine. However, a very simple treatment exists; provision of Vitamin B6 to the patients with this disorder. This was offered to the girls in this family, and symptoms have lessened.

Diagnosis becomes hope and future for the family

In the hospital, the girls’ mother had a bright smile when I met her family again four months later.

She told me that she gave birth to a boy who also suffered from this type of epilepsy, but after he received proper, timely treatment, he is doing well now. When I found out that her newborn son would not suffer the same fate as his sisters, I was very happy indeed.

Anum Shafique's biography

  1. Anum Shafique profile picture
  2. Anum Shafique has an MPhil degree in Biological Science and is completing her PhD degree in Molecular Biology at the School of Biological Sciences, University of the Punjab, Lahore, Pakistan. Studies on molecular analyses of epilepsy are part of her research which is being conducted under the supervision of Professor Sadaf Naz. Anum has identified many families with two or more individuals having epilepsy-related neurodevelopmental issues. Using whole exome sequencing, she has identified genetic causes of the disorders in most of the families. She is currently working on a functional study of one of the variants that she identified during her research at the University of Leeds, UK.

Professor Sadaf Naz's biography

  1. Sadaf Naz
  2. Professor Sadaf Naz is a molecular biologist at the School of Biological Sciences, University of the Punjab, Lahore, Pakistan. The major focus of her research team is on exploring the genetics of recessively inherited, moderate to severe hearing loss, movement disorders, skeletal dysplasias, neurodevelopmental disorders, epilepsy, and psychotic disorders using conventional methods as well as next generation sequencing technology. Personnel in Dr. Naz’s laboratory returns the findings to the participants as appropriate and some of them then use these results by seeking genetic counseling. A few participants have received better treatments due to the genetic diagnoses made available to them; a step in the direction of personalized medicine.

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