With expanded carrier screening, founder populations run the risk of being overlooked.

Genetically isolated populations exist worldwide. Specific genetic disorders, including rare autosomal recessive disorders may have high prevalences in these populations. We searched for Dutch genetically isolated populations and their autosomal recessive founder mutations. We investigated whether these founder mutations are covered in the (preconception) expanded carrier screening tests of five carrier screening providers. Our results show that the great majority of founder mutations are not covered in these screening panels, and these panels may thus not be appropriate for use in founder populations. It is therefore important to be aware of founder mutations in a population when offering carrier tests.

Introduction

The general Dutch population is relatively outbred (Ten Kate et al. 2014). However, several genetically isolated populations exist (for definitions of terms see Box 1). Also, in many other countries worldwide, genetically isolated populations are present. Often these populations are geographically, culturally, or for religious reasons isolated for centuries and as a consequence show less genetic variation. Because of the low genetic heterogeneity, these populations have proven to be very suitable for the identifications of genes involved both in Mendelian as well as in complex disorders. Bottleneck effects in the history of a population and/or founder effects may result in high prevalences of monogenic recessive disorders in these populations compared with the nationwide prevalences.

Box 1

Definitions

Genetically isolated population or founder population: a population that is or was geographically, culturally, or for religious reasons isolated and as a consequence has restricted genetic variation.Bottleneck effect: occurs when there is a sharp reduction in the size of a population due to a natural disaster or similar event with, as a consequence, reduction of the genetic variation in the population.Founder effect: the reduction of genetic variation that occurs when a new population is founded by a small number of individuals (founders) from a larger population and this population remains isolated to other populations.Founder mutation: a gene mutation on an identical haplotype background, observed with high frequency in a genetically isolated population in which one or more of the ancestors were carriers of the gene mutation.Recurrent mutation: a gene mutation on more than one haplotype background, reoccurring multiple times in a population history.

Because of high carrier frequencies in founder populations, carrier screening programs have been introduced in some of these populations. The aim of these programs is to identify carrier couples with a one-in-four risk of affected offspring, enabling autonomous reproductive decision making, which consequently might reduce perinatal morbidity and mortality. Examples are carrier screening programs for genetic disorders in people of Eastern European Jewish (Ashkenazi) descent (for example Tay-Sachs disease) (ACOG Committee on Genetics 2009), targeted carrier screening for severe and frequent disorders in different isolated (mainly Arab and Druze) communities in Israel (Basel-Vanagaite et al. 2007; Falik-Zaccai et al. 2008; Zlotogora et al. 2009), screening for four recessive diseases in the Saguenay-Lac-Saint-Jean region of Quebec, Canada (Tardif et al. 2017), and screening for four severe autosomal recessive disorders in a Dutch genetically isolated community (Mathijssen et al. 2015).

Meanwhile, technological advances have enabled the development and offer of preconception expanded carrier screening (ECS) in which couples without an a priori increased risk of having a child with a genetic disorder can be screened for several (hundreds of) disorders simultaneously (Edwards et al. 2015; Henneman et al. 2016). An increasing number of mainly commercial laboratories offer these screening panels (Borry et al. 2011; Lazarin et al. 2013).

However, the carrier frequencies of several autosomal recessive disorders in genetically isolated populations can be very skewed from nationwide or worldwide carrier frequencies. In some genetically isolated populations, carrier frequencies of disorders which are rare or almost non-existent in the general population may be very high. In contrast, carrier frequencies of more frequent disorders in the general population may be very low in genetically isolated populations.

The aim of this study was to make an inventory of Dutch genetically isolated populations and their autosomal recessive founder mutations, and to investigate whether Dutch founder mutations are covered in the (preconception) expanded carrier screening tests of carrier screening providers.

Methods

We searched for genetically isolated populations in the Netherlands (total population 17 million people) and their founder mutations in the databases PubMed, On-line Mendelian Inheritance in Man (OMIM), and Google semi-systematically by using the keywords “genetically isolated population,” “founder,” “mutation,” “gene,” and “Dutch” or “Netherlands.” Also, 11 Dutch clinical (molecular) geneticists were asked about their knowledge of genetically isolated populations and their specific founder mutations. Only autosomal recessive mutations were included. Recurrent mutations (Box 1) and Dutch founder mutations not related to a specific genetically isolated community were not included (Zeegers et al. 2004). To prevent possible stigmatization, the genetically isolated populations are numbered and the specific names of the villages are not mentioned.

Our purpose was not to be complete, but to illustrate the importance of being aware of founder populations and founder mutations. We therefore made a selection of founder mutations present in different genetically isolated populations for which the most information was available in the literature and from personal information.

Information about the carrier frequencies of founder mutations were derived from the scientific articles and personal communication with clinical (molecular) geneticists. Carrier frequencies in the Dutch general population were derived from The Genome of the Netherlands (GoNL) project (http://www.nlgenome.nl, accessed 24 February 2017) (The Genome of the Netherlands Consortium 2014).

We investigated whether the specific founder mutations were present or absent in the expanded carrier screening panels offered by five ECS providers.

Results

In Table 1, several founder mutations present in six different Dutch genetically isolated populations are shown, including the carrier frequencies of these disorders in the specific genetically isolated population and in the Dutch general population. As can be seen, the carrier frequencies of generally rare disorders are high in these genetically isolated populations.

Table 1

Founder mutations in different Dutch genetically isolated communities and the coverage of these mutations in expanded carrier screening tests

Disorder	OMIM	Disease severitya	Gene	Mutation	Populationb	Carrier frequency genetic isolatec	Carrier frequency Dutch general populationd	Counsyle	GenPath Diagnosticsf	Mount Sinaig	Pathway Genomicsh	Recombinei	References
Fetal akinesia deformation sequence (FADS)	208150	4	MUSK	c.1724T>C p.(Ile575Thr)	1	8.1–11.2%	<0.2%	−	−	−	−	−	Mathijssen et al. (2015) and Tan-Sindhunata et al. (2015)
Osteogenesis imperfecta type IIB/III (OI)	610682	3	CRTAP	c.21_22dupGG p.(Ala8fs)	1	4.1%	<0.2%	−	−	−	−	−	Mathijssen et al. (2015) and van Dijk et al. (2009)
Phenylketonuria (PKU)	261600	3	PAH	c.1315+1G>A	1	9.2%	<0.2%	+	+	+	–j	+	Oorthuys et al. (1985)
Pontocerebellar hypoplasia type 2 (PCH2)	277470	4	TSEN54	c.919G>T p.(Ala307Ser)	1	1.5–14.3%	0.8%	−	−	−	−	+	Barth et al. (1990), Budde et al. (2008), and Mathijssen et al. (2015)
Primary ciliary dyskinesia (PCD)	615067	2	CCDC114	c.742G>A p.(Gly248Thrfs)	1	10%	0.4%	−	−	−	−	−	Onoufriadis et al. (2013)
Pseudoxanthoma elasticum (PXE)	264800	3	ABCC6	c.3775delT p.(Trp1259Glyfs)	1	15 cases described (~21,500)	0.8%	−	–j	−	−	−	Bergen et al. (2000) and Plomp et al. (2009)
Retinitis pigmentosa type 12 (RP12)	600105	2	CRB1	c.3122T>C p.(Met1041Thr)	1	4.1%	<0.2%	−	–j	+	−	−	Den Hollander et al. (1999) and Mathijssen et al. (2017)
Rhizomelic chondrodysplasia punctata type 1 (RCDP1)	215100	4	PEX7	c.875T>A p.(Leu292X)	1	6.1%	<0.2%	+	+	+	−	+	Mathijssen et al. (2015)
Van Buchem disease (VBCH)	239100	3	SOST	52 kb deletion approximately 35 kb downstream of gene	2	≥13 cases described (~20,000)	<0.2%	−	−	−	−	−	Balemans et al. (2002) and Van Buchem et al. (1955)
Congenital retinal dystrophy	204100	2	RPE65	c.1102T>C p.(Tyr368His)	2	3.1–7.7%	0.4%	−	−	+	−	+	Schappert-Kimmijser et al. (1959) and Yzer et al. (2003)
Retinitis punctata albescens (RPA)	136880	2	LRAT	c.12delC p.(Met5CysfsX53)	2	4 cases described (~20,000)	<0.2%	−	−	−	−	−	Littink et al. (2012)
Vici syndrome (variant form)	242840	4	EPG5	c.4862G>A p.(Arg1621Gln)	2	±10% (pc)	<0.2%	−	−	−	−	−
Benign recurrent intrahepatic cholestasis (BRIC)	243300	2	ATP8B1	c.2932-3C>A, skipping of exon 24	3	≥7 cases described (~20,000)	<0.2%	−	−	−	−	−	De Koning et al. (1995), Houwen et al. (1994) and Klomp et al. (2004)
Chudley-McCullough syndrome (CMCS)	604213	2	GPSM2	c.1473delG p.(Phe492SerfsX5)	4	3 cases described (~15,000)	<0.2%	−	−	−	−	−	Almomani et al. (2013) and Hendriks et al. (1999)
Juvenile neuronal ceroid lipofuscinosis (CLN3)	204200	4	CLN3	1.02 kb deletion	5	17 cases described	0.5%	+	−	+	−	−	Taschner et al. (1995)
Parkinson disease type 7 (PARK7)	606324	3	DJ-1	14 kb deletion	6	0.9%	<0.2%	−	−	−	−	−	Bonifati et al. (2003)

“+” presence of the mutation in panel. “−” absence of the mutation in panel, pc personal communications

aDisease severity; 1 = mild, 2 = moderate, 3 = severe, 4 = profound (Lazarin et al. 2014). Scored independently by IM and IK. Discrepancies were discussed until consensus was reached

bSix different Dutch founder populations (coded from 1 to 6)

cIf the carrier frequency in the genetically isolated community is not known, the number of cases described in the literature and the current population size of the genetically isolated community is noted

dDerived from Genome of the Netherlands (GoNL) project, http://www.nlgenome.nl; accessed 23 February 2017

eFamily Prep Screen (113 disorders); https://www.counsyl.com/services/family-prep-screen; accessed 6 February 2017

fInheriGen Plus (167 disorders); http://www.genpathdiagnostics.com/womens-health/inherigen; accessed 6 February 2017

gNextStep Pan-Ethnic Carrier Screen (281 disorders); http://nextsteptest.com; accessed 6 February 2017

hCarrier Status DNA Insight (72 disorders); https://www.pathway.com/carrier-status-dna-insight; accessed 6 February 2017

iCarrierMap (315 disorders); http://www.recombine.com/carriermap; accessed 6 February 2017

jA selection of mutations is included in the carrier screening, but the founder mutation is not

For the five selected carrier screening providers, the coverage of 16 founder mutations in the carrier screening tests is shown. For each carrier screening provider, on average 2.8 (range 0–5) of the 16 founder mutations are covered in the test. Eleven (69%) of the founder mutations are covered in none of the five carrier screening tests. In the test of two providers, a selection of mutations in the specific gene of three disorders is included in the carrier screening test, but the founder mutation is not.

Discussion

In genetically isolated populations, carrier frequencies of genetic disorders can be very different from the carrier frequencies in the general population. The great majority of these founder mutations are not covered in the ECS panels of the five selected providers. This also applies to most of the founder mutations present in genetically isolated populations in other countries.

Offering a (commercial) routine ECS panel to inhabitants of these genetically isolated populations is not appropriate because it may give false reassurance to couples with an increased risk for founder mutations related disorders they are not being tested for.

For a reliable carrier test offer, it is therefore important to know the genetically isolated populations and their founder mutations in each country. Nationwide databases in which the genetically isolated populations, their relatively frequent genetic disorders, and the specific genes and mutations are listed, are a suitable solution. A database is not only very important for carrier screening programs but also for making a rapid (differential) diagnosis by clinicians, genetic counseling, and research in these populations. For some genetically isolated populations such (online) databases are already available. Examples are the Amish, Mennonite, and Hutterite Genetic Disorder Database (www.biochemgenetics.ca/plainpeople) (Payne et al. 2011) and the Israeli National Genetic Database (www.goldenhelix.org/israeli) (Zlotogora 2010).

Ideally, a customized carrier test will be developed for each country/region in which both country/region-specific mutations as well as genetic isolate-specific founder mutations are present. This approach may also reduce potential stigmatization of genetic isolates, while specific mutations still are included.

In the Netherlands, carrier screening is only (partly) paid by health insurance companies in case of an increased risk of being a carrier; e.g. carrier screening for four autosomal recessive disorders in a genetically isolated community (Mathijssen et al. 2015) and carrier screening for nine disorders in individuals of Ashkenazi Jewish descent (Holtkamp et al. 2016). Recently, the Academic Medical Center in Amsterdam started a non-profit offer of carrier screening for 50 severe autosomal recessive disorders. Most of the severe disorders currently known in Dutch genetically isolated populations are included. Probably, in a non-commercial setting, it will be more likely to take into account the founder mutations present in founder populations than for commercial companies to include those mutations.

It is expected that in the near future, it will become possible to use whole-exome sequencing (WES) or whole-genome sequencing (WGS) for ECS, in which all known disease genes can be screened, including very rare disease genes prevalent in genetically isolated populations. However, correct interpretation of test-results (e.g. variants of unknown clinical significance) when using WES or WGS is complex. Also, the identification of carrier couples for mild disorders which are unlikely to alter reproductive plans is an important point to take into consideration (Beaudet 2015; Sallevelt et al. 2016).

In the meantime, descendants from genetically isolated populations should be made aware that a (commercial) routine ECS panel may not be appropriate and can give false reassurance because the population-specific genes and/or mutations are not covered. Currently, this information is not mentioned by expanded carrier test providers.

Not only genetically isolated populations but also consanguineous couples and populations with a high rate of consanguineous unions have an increased risk of having a child with an autosomal recessive disorder (Teeuw et al. 2014). Many of these disorders are rare disorders which are also not covered in the (commercial) routine ECS panels. These panels may therefore also not be appropriate for use in consanguineous couples and in countries/populations with a high rate of consanguineous unions.

Conclusions

In genetically isolated populations, carrier frequencies of generally rare autosomal recessive founder mutations can be very high. The great majority of these founder mutations are not covered in most (commercial) routine ECS panels. It is important to be aware of founder populations and founder mutations when using these ECS panels and to check whether the mutations are covered. If these founder mutations are not covered, customized screening tests should be developed which include the founder mutations.