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UConn Study Suggests SNP Arrays Add Value to Recurrent Pregnancy Loss Diagnosis

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NEW YORK (GenomeWeb) – A study by researchers from the University of Connecticut has found that SNP microarray testing performed on formalin-fixed paraffin-embedded samples is a promising tool for evaluating recurrent pregnancy loss in couples who haven't already had other cytogenetic testing.

Results of the study, published last month in the Journal Obstetrics and Gynecology, also suggested that the routine use of SNP arrays to test preserved products of conception (POC) samples could help rule out cases of pregnancy loss due to fetal aneuploidy, and thus increase the diagnostic yield of follow-on screening tests used to provide answers to couples with unexplained multiple lost pregnancies.

Bat-Sheva Maslow, the first author of the study and a UConn instructor and clinician, told GenomeWeb this week that when couples are referred to fertility clinics like UConn's Center for Advanced Reproductive Services after the loss of multiple pregnancies, it is most often long enough after they have suffered their most recent miscarriage that fresh tissues from that pregnancy loss are no longer available.

The currently recommended screening process for these patients involves a variety of evaluations including parental karyotypes, maternal serum testing, and evaluation of the uterine cavity. These procedures  can be expensive, and, more importantly, only identify a causal disorder or illness in a fraction of cases.

"We are essentially an infertility clinic, but we also have patients referred to us because they've had multiple losses. They aren't infertile. They are able to get pregnant, but for whatever reason they haven’t been able to maintain the pregnancy," Maslow explained. 

"When you see these patients, the classic [procedure] is to run this battery of testing on the couple looking for inherited thrombophilias, or autoimmune disorders, or something in the uterine cavity — all of which have very low prevalence, and so the yield of these tests is very low," she added. "Somewhere near 90 percent of patients go through this battery of testing and we say, 'OK everything is normal,' and we have nothing else to offer them. It's frustrating both for us as providers and also for patients. We know from the get go that we are unlikely to find a useful answer."

Until recently, genomic technologies were not available for testing of preserved POC tissue samples, but that has changed, opening up the possibility of adding chromosomal array or other genomic analyses to the current cadre of recommended tests, Maslow said.

"That was a game changer, so now we can look at the tissue and if there is a chromosomal abnormality we can tell the parents, this is why you had this loss. There may or may not be any treatment, but at least we can tell them, this is what happened," she explained.

Moreover, by identifying pregnancy losses due to fetal aneuploidy, use of these genomic tests as a first line could help rule out those easier answers, focusing the standard battery of other screening tests on a smaller, higher-risk population, where they should have a much higher diagnostic yield, Maslow and her colleagues hypothesized. 

"If the SNP testing reveals that a loss is euploid, that's a pregnancy that should have progressed and it didn't for some other reasons. So that's a smaller population in which we can be more aggressive in terms of testing and maybe empiric treatment," she said.

In their study, Maslow and her colleagues set out to try to accurately measure the relative success rate of SNP array testing versus the standard practice, and to explore some of these other questions.

Retrospectively, the investigators compared results of the standard recommended screening process and the results of SNP array testing of FFPE POC samples for a group of 42 women in order to determine their relative detection rates.

During the study's recruitment, physicians at the UConn Center for Advanced Reproductive Services began routinely requesting FFPE POC samples from patients, and when available, sending these for SNP array analysis by Natera, which offers a POC testing service it calls Anora.

While UConn has adopted Natera's test, Maslow stressed that the company is not the only one with technology able to perform chromosomal array analysis of FFPE POC samples.

In addition to SNP arrays, the field has also adopted array-CGH for POC testing, and Maslow said that to her knowledge, the choice of these technologies varies from provider to provider.

In their study, Maslow and her co-investigators took the results of Natera's SNP-based chromosomal array analysis, and results of the standard screening methods for their cohort of 42 couples, defined a detection rate for each, and then compared them.

As expected, Natera's Anora analysis had a higher success rate in detecting a cause for pregnancy loss than did the standard screening procedures. The detection rate was 0.5 for the array testing and only 0.17 for the standard screening methods.

When the group looked only at subjects with a single FFPE POC sample available, to account for any potential bias in analyzing multiple samples from some women in the study, they found that the detection rate for SNP array testing remained significantly higher than for recommended screening — 0.52 versus 0.11.

Based on the group's data, it also looked like performing array-based chromosomal testing on POC samples as a first step in the testing process could help rule out women with pregnancy losses due to fetal aneuploidy, avoiding unnecessary further testing in these couples and increasing the rate of diagnosis using the recommended screening tests in the remaining patients. 

For example, 14 women in the study had at least one euploid loss, based on the POC SNP testing results. Of these, five had a positive result from the recommended recurrent pregnancy loss evaluation process. In other words, by ruling out miscarriages due to fetal aneuploidy, the diagnostic yield of this screening process could be increased to 35 percent from the 17 percent demonstrated in the overall cohort. 

Maslow said that the current process for evaluating women at the UConn center varies from provider to provider, but that many clinicians have adopted SNP-array testing into their practice as an initial screen to identify aneuploid and euploid cases before moving on to the recommended cadre of other evaluation methods.

The team's study, though the largest done so far, was still small, she said, and it will be important for more data to be collected, ideally in a multi-center setting, to solidly define the yield and the potential added value of FFPE POC chromosomal array analysis.

"We'll need more data before we could really change practice widely, but on a small scale [the results were] really what we expected," Maslow said. "Everyone who treats recurrent pregnancy loss finds it frustrating that the current standards are so low-yield. But till now we didn't have anything else to really offer patients, so this gives us at least one more tool to be able to tackle that frustrating clinical problem."

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