For prenatal NGS labs, new accreditation requirements

Anne Paxton

September 2013—With the 2013 edition of the Laboratory Accreditation Program checklist, the College moves to a new level in its effort to ensure the highest-quality practices in clinical laboratories’ use of next-generation DNA sequencing.

Expanding on last year’s debut of next-generation sequencing checklist requirements, the new molecular pathology checklist, released July 29, includes a focus on NGS for maternal plasma to identify fetal aneuploidy. Phase I requirements address information needed on requisitions, monitoring of assays and targeted disorders, and reporting, while phase II requirements address quality control.

Noninvasive prenatal screening is the right place to start in setting detailed checklist requirements for NGS, says Glenn Palomaki, PhD, a member of the Biochemical and Molecular Genetics Resource Committee of the CAP and American College of Medical Genetics and Genomics. “This is by far the largest application for NGS right now. It is likely that more pregnant women are going to choose to have this test in the coming year than all the other tests using NGS technology.”

In the U.S., the new NGS prenatal section will be applicable to just four companies: Sequenom, Verinata Health, Natera, and Ariosa Diagnostics, which are the only laboratories that currently offer noninvasive prenatal screening based on circulating cell-free DNA. A few other CAP-accredited laboratories offer the testing outside the United States.

“In 2012, we published the first checklist requirements specifically for next-generation sequencing,” says Karl Voelkerding, MD, chair of the CAP NGS Work Group and professor of pathology, University of Utah, and medical director for genomics and bioinformatics, ARUP Laboratories. “The requirements were written so that they could generally apply to genetics/inherited disorders, oncology, and other emerging NGS-based testing areas. But we didn’t divide them into specific areas.”

“Now the process is that each year, when the overall CAP checklist is published, we will incorporate specific, topic-focused accreditation requirements. This year our NGS Work Group was asked to review the area of using NGS to screen for fetal aneuploidy in pregnant women.”

The added checklist requirements are new for laboratories doing NGS testing, says Dr. Palomaki, an epidemiologist who has been working in prenatal screening for more than three decades.

“The new requirements are modeled after those already in the chemistry checklist,” he says. For the 200 to 300 maternal serum screening laboratories in the U.S. that have been operating for the past 20 years, the data collection, monitoring, and QC parameters would not be considered new. “But much of this will seem new to the four prenatal NGS companies.”

The NGS Work Group that helped develop the checklist additions didn’t want to be highly prescriptive. “We didn’t want to mandate that everyone ought to follow the checklist exactly,” says Dr. Palomaki, who was a contributor to the group. But the hope is that the laboratories performing prenatal NGS, given guidance from the checklist, will head in the right direction and gain useful clinical information from the data collection as well.

For example, the new checklist requirement (MOL.34915) that requisitions include a gestational age estimate, based on either ultrasound measurements, first day of last menstrual period, or estimated date of delivery, is important because clinical validation studies have been conducted mainly on samples drawn over 10 to 20 completed weeks’ gestation, Dr. Palomaki points out.

If requisitions show a lot of samples being collected at 24 weeks, or before 10 weeks, it could indicate a new use for what is considered a screening test. “You might want to investigate if more than a certain percentage of samples are from late in gestation. If a large number are being done later, labs may want to document these new patterns of practice so we can detect inappropriate testing. Alternatively, there may be a whole new way to use this test that we’re not anticipating.”

Maternal weight, another piece of the clinical history now required on requisitions in checklist item MOL.34917, may be even more significant, because it has a strong impact on fetal fraction. The analytic performance is reduced when fetal DNA levels are inadequate. “It’s not as simple as a dilution effect,” Dr. Palomaki explains. “But in fact, for women over 130 kg [285 lbs], the test has about a 50 percent failure rate. So you can reach the point where it may not be reasonable to offer the test.”

“I don’t think any professional standards have emerged as to how this issue should be handled. Should physicians routinely inform women over a certain weight that the test is more likely to fail? Should the test not be offered to women over a certain weight?” Although the ACMG and the American Congress of Obstetricians and Gynecologists have said maternal weight is an important factor, neither has made recommendations on how to take it into account, Dr. Palomaki says.

“So clearly we’d like to have more information about this relationship. The commercial laboratories should be looking over their data to see if there is a maternal weight above which they’re unhappy with the proportion of successful tests. They may decide they want to say something in their educational materials.”

Another situation in which more information would be helpful is that of multiple gestations. Data about multiple gestations are required (MOL. 34919), if the laboratory accepts such samples.

“We have a limited experience with twins, and it is probably up to the laboratory whether it feels confident in offering the screening to this population. There’s insufficient information to justify screening triplets at this time, but we’d like to learn more about twins,” Dr. Palomaki says.

Even more complicated are in vitro fertilization cases. The checklist (MOL.34918) recommends collecting parentage data, because closer scrutiny is needed. “IVF pregnancies are sometimes associated with an early fetal demise or a ‘vanished twin.’ What if the vanished twin had Down syndrome?”

While the test may work perfectly well in this group, he says, “this is a population of women who are very concerned about their pregnancy and very much want to avoid an invasive procedure with its associated potential for fetal loss. This group is also more likely to have the resources to afford a test like this. There is an extra onus on the community to make sure that for this vulnerable group, the test works well.”

The new checklist also requires collecting data about family history and prior pregnancy risk (MOL.34920 and MOL.34922). While some companies offer the test only to high-risk patients, others will perform the test for women in the general pregnancy population. Given this wide range in prior risks, laboratories should at least have this information available when making an interpretation, Dr. Palomaki says.

“For example, should the DNA test in a 30-year-old with a negative serum screening test be interpreted the same way as a 38-year-old with a positive integrated test? Are they simply ‘positive’ or ‘negative?’ The interpretation should account for the prior risk, when possible.