Rare lethal disorder traced to variant of the PIGA gene on the X chromosome

Next generation sequencing plays key role in biochemical discoveries

By Raymond MacDougall
Associate Communications Director for Intramural Research
Chromosomes

Next-generation genomic sequencing — technologies that streamline the processing and analysis of DNA — are well suited to rare disease discovery, as a recent study led by National Human Genome Research Institute (NHGRI) researchers demonstrates.

A team of clinical and bench researchers, including colleagues at the Johns Hopkins University and Children's National Medical Center, used next generation genomic sequencing, in addition to classic biology, to find a variant in a gene that causes a devastating and rare disorder in newborns. Their study was published in the February 2, 2012 issue of the American Journal of Human Genetics.

The research study focused on DNA from a single family. Two brothers inherited a faulty version of the gene on the X chromosome that makes a molecule called phosphatidylinositol glycan class A, or PIGA. This genetic alteration caused developmental problems, including malformations of the skeleton, heart and brain. The two brothers died within weeks of their birth, both from respiratory complications. Females in the same family may carry the mutation in their genome but are unaffected.

"This newly recognized disease is caused by a mutation in a gene that was previously only associated with a rare blood system disorder," said Leslie G. Biesecker, M.D., senior author and chief of NHGRI's Genetic Disease Research Branch.

The PIGA gene is familiar to many who have studied medicine or genetics because of its association with a rare mosaic blood disorder known as paroxysmal nocturnal hemoglobinuria (PNH), according to Dr. Biesecker.

A mosaic disorder is one that arises during embryonic development and affects only the line of cells that result from division of a single cell that mutates during cell division. In the case of the newly identified condition, however, this mutation was present in all of the brothers' cells because they inherited it from a parent.

In PNH, a chronic condition that can occur at any age, blood cells break down over time and leak hemoglobin. One symptom of this leakage of hemoglobin is dark discoloration of urine that concentrates overnight. While it is associated with complications that might shorten the lifespan, the severity of a PIGA mutation that leads to PNH is not as devastating as the newly identified disorder, because it affects a subset of cells in the body.

When the newly discovered PIGA gene mutation passes from parents through the lone X chromosome of a male child, all of the boy's cells are affected. The cells lose the function of a key molecule necessary for anchoring other proteins involved in cell structure and function. The researchers hypothesized that the mutation reduces, but does not eliminate, the function of the protein coded by PIGA, so that survival of an embryo and of a fetus is possible. But the reduced function is not sufficient for a child to survive for long.

The findings from this study have provided novel insights into the biology of a new disorder and may also benefit a family devastated by the loss of their children, according to Jennifer Johnston, Ph.D., lead author and NHGRI staff scientist. Partnership with the family played a crucial role in this discovery.

"DNA sequencing offers answers that will be important for succeeding generations in the same family," she said. "We identified the cause of a condition that has a very bad outcome, and the family needed answers. Our hope is that this discovery will benefit other families in the future by helping their clinicians arrive at a faster diagnosis and sparing them a diagnostic odyssey." The research team dedicated the study to the memory of the deceased boys.

How next-generation genome sequencing played a central part in the discovery

Research to pinpoint the genetic cause of a rare disorder is much like finding the proverbial needle in a haystack. After all, there are 3 billion base pairs in the human DNA code and about 21,000 protein-coding genes that genomic researchers must sift through to find the error that causes a particular disease.

Genomic sequencing has become faster, cheaper and more readily available. Annotations describing the function of DNA code are being accumulated and datasets that include DNA sequence from various study populations are available for comparison.

"The technology is very useful for identifying the genetic cause of many hereditary rare disorders," said study co-author Jamie Teer, Ph.D., NHGRI postdoctoral fellow. "It is actually slightly easier to identify rare genetic variants because you will not see the variant in the population that doesn't have the disorder — the general population. By eliminating common variation, your list of potential disease causing variants for a rare disease is much smaller."

Researchers who conduct genomic sequencing and analysis in order to identify disease variants in genes often need not hunt through the entire human genome. They can often reduce the amount of data by sequencing just the protein-coding regions of the genome, or exome, which is less than two percent of the entire genome. In the present study, the sequence of just the exon regions of the X chromosome was required.

According to Dr. Teer, rare diseases also are often studied by researchers because such study provides insight about more common disorders. In the case of the PIGA gene mutation disorders, the more common disorder helped inform the rare condition, because the gene function is well established. When researchers identify the genetic cause of rare diseases, they also improve knowledge of biological processes, diseases and potential for treatments.

Although a treatment strategy is not immediately available for the rare germ line PIGA mutation disorder, the identity of a disease mutation can provide a starting point to target treatment.

Investigations of rare disorders will continue to be a focus of research, even as technologies to scrutinize them improve. Plus, availability and access to genomic sequencing is increasing. "People are beginning to apply next-generation sequencing to anything that may have genetic contributions," Dr. Teer said. "It can't be too long before genomic sequencing starts to shift into general clinical practice."

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Last Reviewed: August 7, 2012