Tag Archives: carrier screening panels

ACMG Carrier Screening Guideline: The Hypothetical “Tier 3” Panel

This post was modified on 3/30/2022 with input presented by some DNA Exchange readers.  First – the original post did not account for the fact that ELP1 is reported out as IKBKAP by Natera, SEMA4 and Quest. Table and graph were updated to reflect this. 

While the list of labs surveyed for this post was not intended to include all labs that offer carrier screening, it has been noted since this was initially posted that Fulgent does offer a carrier screening panel based on the ACMG Tier 3 recommendation. A paragraph has been added to reflect Fulgent’s test offering.

In July 2021, the American College of Medical Genetics and Genomics published a new carrier screening guideline, Screening for autosomal recessive and X-linked conditions during pregnancy and preconception: a practice resource of the American College of Medical Genetics and Genomics (ACMG). The gist of this recommendation is that all individuals who are considering pregnancy or who are pregnant should be offered a carrier screening panel inclusive of 113 specific genes. In a prior post, Bob Resta and I shared our concerns regarding ethical issues and the ways in which this panel was designed.

With this post I have a practical question regarding implementation: How does one order a carrier screening panel of these ACMG-recommended genes when such a panel does not exist?  

A quick recap of the ACMG carrier recommendation. The guideline defines 4 tiers of carrier screening:

Carrier Screening Tiers defined in the ACMG Practice resource, Screening for autosomal recessive and X-linked conditions during pregnancy and preconception: a practice resource of the American College of Medical Genetics and Genomics (ACMG).

The carrier frequencies utilized are based on the public database gnomAD and represent carrier frequencies for any subpopulation that makes up at least 1% of the United States total population. 

The goal of this ACMG recommendation was to define a standard panel that could be offered to all patients. The guideline recommends that all patients who are pregnant or are considering pregnancy be offered the “Tier 3” panel, and that reproductive partners may also be offered the Tier 3 panel simultaneously. This panel is inclusive of 113 genes, 86 of which were derived from the gnomAD data as having a carrier frequency of 1 in 200 or higher; 11 additional genes were  “highly represented in one or more patient populations and have potential to be underrepresented in gnomAD”; and 16 genes associated with X-linked conditions with a prevalence of 1 in 40,000 or higher.

ACMG recommends against using the Tier 1 or Tier 2 panel for any patient. Further, it states that the Tier 4 panel be reserved “for consanguineous pregnancies (second cousins or closer) and in couples where family or medical history suggests Tier 4 screening might be beneficial.”

A huge problem with this recommendation is that the Tier 3 panel, as it is described by ACMG, does not exist as an orderable test through most labs. I have surveyed several labs, and those with the biggest commercially available panels do not provide coverage for somewhere between 25 and 49 genes of the 113 that are outlined by ACMG for the Tier 3 panel.  

Analysis of carrier screening labs performed on March 24, 2022. For a full list of genes by lab, see Table below. 

Some of the labs I have highlighted in this analysis have published press releases and sent emails to their client base in enthusiastic support of these guidelines that call for expanded carrier screening, even though NONE of them actually offer what ACMG currently recommends. The Industry lobbying group for Myriad, Natera, SEMA4 and ThermoFisher, the Access to Equitable Carrier Screening Coalition “applauds American College Of Genetics And Genomics” on this new recommendation that none of these labs can currently fulfill.  

One lab, Fulgent Genetics, offers a panel that is based on the Tier 3 recommendation, along with several caveats and limitations for some of the recommended genes that have common variants that may be missed or are expected to escape detection by their platform. While the Fulgent panel includes  all 113 ACMG-recommended genes, these caveats and limitations demonstrate that sensitivity across the genes included can vary dramatically and may be low in cases where the common mutation is a trinucleotide repeat, inversion or other alteration not reliably identified through next generation sequencing.  For example, Fulgent reports including FXN analysis on their panel with the caveat that their analysis will only detect sequence variants  which account for <5% of pathogenic  variants in this gene (the vast majority of FXN pathogenic variants  are due to GAA repeat expansion.)

Perhaps Fulgent along with other labs that are working to develop a panel that meets the ACMG requirements and will be able to identify most pathogenic variants in the 113 gene set.  It may be difficult to do this and keep the cost of testing down as there are technical challenges to assessing some of the genes that ACMG recommends. For example, the most common mutation in the F8 gene is a gene inversion. With PLP1 the most common mutation is a gene duplication. Rearrangements are common with the OCA2 gene. These technical variations present a challenge to labs as they expand their carrier screening panels. From the marketing perspective, adding 50 genes to their currently existing platform may seem more impressive than adding a small handful of more technically difficult ACMG-recommended genes.

Do obstetrical care providers recognize that when they are ordering an expanded panel that it may include hundreds of genes that are not recommended while missing several genes that are part of this ACMG-produced panel? What does this mean for our liability as providers when we cannot order a test that is recommended by our professional society? 

In a future post I plan to focus on carrier screening for cystic fibrosis and some of the harm seen from reporting practices on expanded carrier screening. But for now I would like to reflect back to the time when we first considered screening for cystic fibrosis, the rollout of which was not without challenges. Before guidelines were issued by the American College of Obstetricians and Gynecologists and the American College of Medical Genetics, there was significant preparation for implementation. Care was taken to determine whether we knew that the variants included on the CFTR panel cause disease. We thought we were clear about this but even with great scrutiny, the original 25 mutation panel included a variant that we eventually learned did not cause disease. There were standards written for laboratories regarding how to do the testing and what should be included in the report. There were educational resources developed for patients and providers. There appears to be much less care and preparation with these current guidelines in spite of the recommendations for testing for many more as well as increasingly complex conditions.

In today’s world of carrier screening, we see both the 113 gene Tier 3 panel recommended by the ACMG as well as commercial laboratories in constant competition to expand the size of their carrier panels. Yes, labs are expanding their genetic carrier screening offerings, but it does not appear (regardless of their marketing materials) that the recommendations from ACMG are the reason why. Even some of the biggest panels available don’t include 22-43% of the genes recommended by the ACMG while providing coverage for numerous genes that are not included in the recommendation. Data regarding performance characteristics of screening for many of these genes both within and beyond the panel are lacking. As a result, pre and post test counseling our patients regarding carrier screening and the downstream challenges are just going to become increasingly more complex.  

ACMG Tier 3 Panel
Labcorp / Integrated Inheritest® 500 PLUS Panel
SEMA4 Expanded Carrier Screen (502 Genes)
Natera Horizon™ 421
Myriad Foresight®
Invitae Comprehensive Carrier Screen
Quest QHerit(R) Extended
ABCA3
ABCC8
ABCD1
ACADM
ACADVL
ACAT1
AFF2
AGA
AGXT
AHI1
AIRE
ALDOB
ALPL
ANO10
ARSA
ARX
ASL
ASPA
ATP7b
BBS1
BBS2
BCKDHB
BLM
BTD
CBS
CC2D2A
CCDC88C
CEP290
CFTR
CHRNE
CLCN1
CLRN1
CNGB3
COL7A1
CPT2
CYP11A1
CYP21A2
CYP27A1
CYP27B1
DHCR7
DHDDS
DLD
DMD
DYNC2H1
ELP1
ERCC2
EVC2
F8
F9
FAH
FANCC
FKRP
FKTN
FMO3
FMR1
FXN
G6PC
GAA
GALT
GBA
GBE1
GJB2
GLA
GNPTAB
GRIP1
HBA1
HBA2
HBB
HEXA
HPS1
HPS3
IDUA
L1CAM
LRP2
MCCC2
MCOLN1
MCPH1
MID1
MLC1
MMACHC
MMUT
MVK
NAGA
NEB
NPHS1
NR0B1
OCA2
OTC
PAH
PCDH15
PKHD1
PLP1
PMM2
POLG
PRF1
RARS2
RNASEH2B
RPGR
RS1
SCO2
SLC19A3
SLC26A2
SLC26A4
SLC37A4
SLC6A8
SMN1
SMPD1
TF
TMEM216
TNXB
TYR
USH2A
XPC
As of March 23, 2022

Quest Diagnostics QHerit™ Extended

Myriad Foresight® Carrier ScreenUniversal Panel

Invitae Comprehensive Carrier Screen

Labcorp / IntegratedInheritest® 500 PLUS Panel

SEMA4 Expanded Carrier Screen (502 Genes)

Natera Horizon 421 (from printed materials provided by Natera)

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Screening Everyone For Everything: A Changing Model of Screening For Carrier Status of Genetic Diseases?

The heterozygote carrier screening paradigm  is  starting to shift from ancestry based screening  for carriers of a single or a few genetic diseases to pan-ethnic screening for carriers of a wide range of genetic diseases. New techniques of DNA sequencing make it possible to test a single sample to determine carrier status for dozens of genetic conditions at prices that make carrier screening panels (CSPs) very tempting to healthcare providers and patients. Since carrier screening for one or another genetic disease – cystic fibrosis, Tay-Sachs, hemoglobinopathies – is already offered to essentially all women who are pregnant or planning a pregnancy, why not “screen everyone for everything” at no greater up front cost? And it doesn’t even require a blood sample; a less intimidating buccal sample works just fine.

Part of the understandable justification to move beyond targeted carrier screening programs is the futility of trying to classify people into distinct ancestry/racial/ethnic categories. Gene mutations and genetic diseases have a pesky habit of flowing fluidly between populations, and cultural heritages can be lost through assimilation (See Interesting Digression* below).

People

So why object to CSPs? After all, don’t people have a right to “know their DNA” and to understand what health and reproductive risks they face?

I am not suggesting that we should stand in the way of anyone’s wishes to “know their DNA.” If someone chooses to acquire that knowledge without the benefit of meeting with a genetic counselor, well, I may disagree with that decision but I respect it. But whether people decide to undergo carrier testing through a genetic counselor or through an online testing company, they need information that is forthright, complete, and transparent; they do not need subtly biased sales pitches. Private companies do not have a vested interest in talking people out of genetic testing.

Before we examine how some labs “objectively” describe carrier screening to patients, we must acknowledge an ethically uncomfortable truth. Carrier screening does not consistently lead to better treatments,  encourage greater tolerance of disabilities,  stimulate research into cures, or improve psychosocial adaptation to genetic disease. The only compelling reason to devote economic and medical resources to carrier screening is to reduce disease incidence. For better or worse, that is the measure of success of Tay-Sachs screening in Ashkenazi Jews and thalassemia screening on Cyprus.

Three strategies can reduce the incidence of genetic disease. One is mate selection based on carrier status, which is rare except in select populations such as Ultra-orthodox Jews (Hey Single Women out there, when was the last time you met potential Mr. Right and said “Er, you can buy me a drink but do you mind if I take a pedigree and a cheek swab from you before I give you my phone number?”). A second approach is preimplantation genetic diagnosis, but it is available to only a miniscule percentage of the population. The third and only realistic option for most patients is the elephant in the room – prenatal diagnosis with termination of affected fetuses.

Bar

Take a look at the  web sites of companies such as Counsyl or 23andMe and you get a different narrative. The word “abortion” does not appear. Instead, you read about sperm/ovum donation, preimplantation diagnosis, mental preparation, watchful waiting, and early treatment. No mention is made that early treatment requires testing the baby anyway and that some treatment is available for only a handful of the screened conditions. The websites do not bring up the point that there are no large-scale studies that have shown better familial adaptation to genetic disease when parents have prenatal awareness of their carrier status, so couples really cannot know if testing really will result in mental preparedness. And I am still not sure what watchful waiting is, and how it differs from mental preparedness.

waiting

A second concern is that screening for very rare conditions plays on the emotionally vulnerable state of many pregnant women and the difficulty almost anyone has in understanding very, very small numbers in a psychologically meaningful way. Take for example, a condition that has an incidence of 1/100,000 births with a 75% carrier detection rate. Before carrier testing, a couple would have an ~99.9999% of NOT having an affected child; after carrier testing that probability would increase to ~99.99999%. Really, who can tell the difference between those two statistics? It’s difficult just trying to count the number of nines in those numbers. But read about the condition’s severe intellectual disabilities and physical birth defects, and, damn the statistics, give me that test.

A third concern is the lack of complete information about test sensitivity on the information portion of the website. For example, a patient with normal carrier test results might understandably think they would not have to be concerned about having a child with Bardet Biedl syndrome. What the site does not indicate however is that BBS1 and BBS10, the two loci included in the  panel, account for less than half of patients with Bardet Biedl syndrome, and that the dozen or so other genes that can cause Bardet Biedl syndrome are not included in the test panel.

A fourth, and maybe the greatest, concern is the ethical difficulty of deciding which conditions to include on a CSP. Tay-Sachs screening among Ashkenazi Jews and thalassemia screening in Cyprus developed with significant input from families, medical professionals, and community and religious leaders. There was widespread agreement in those communities that these were serious diseases and that carrier screening, mate selection, or prenatal diagnosis were ethically acceptable ways of reducing disease incidence. Very little community dialogue has taken place over CSPs. Do we really believe that the world is a better place if we screen for carriers of a common form of hereditary deafness or, God help us, red hair color?

Redhead

And ruminate on this: a study of 3 million cystic fibrosis carrier tests performed at a single US lab found that 25,000 CF carrier screens needed to be performed to detect one affected fetus. And this is for a relatively common genetic condition with a frequency of about 1/4000 US newborns and  a screening program whose success remains debatable. How many carrier screens will need to be performed to detect a fetus or newborn with a rare disorder like isovaleric academia, with a frequency of 1/250,000 births?

It could be that I am just the last of the old wave of genetic counselors who are out of touch with new technologies and changing ethical values, the proverbial last leaf on the tree. Maybe I am a 20th century genetic counselor in a  21st century world in which private industry will become the primary mode for the delivery of medical genetic services. Perhaps when I retire in a decade or so the genetic counseling community will issue a collective sigh of relief. But sometimes Old School cranks have a point.

MR900400816

* – Interesting Digression: I recently learned about the Jews of Acadiana, Jewish merchants who settled among, and who were often culturally and reproductively assimilated into, Louisiana’s Cajuns (although the Cajun Tay-Sachs mutations stem from their French Canadian origins and predates the Ashkenazi admixture). Also, an exploration of why Tay-Sachs screening caught on among Ashkenazi Jews but not among Cajuns would make for  an interesting socio-medical-historical study. If a  large scale  Tay-Sachs screening program were to be introduced among Cajuns, perhaps its motto would be Laissez les bon genes roulez.

Accordion

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