Whole exome sequencing identifies novel pathogenic variants in TGM1 and ALOX12B in patients with hereditary ichthyosis

BACKGROUND

Hereditary ichthyosis is a clinically and genetically heterogeneous disorder associated with more than 50 genes with TGM1, ALOX12B, and ALOXE3 being the most prevalent. Establishing an accurate diagnosis is important for effective genetic counseling and optimal patient management.

OBJECTIVE

We studied the diagnostic value of whole exome sequencing (WES) in a small case series with hereditary ichthyosis.

METHODS

During a 1-year period, index cases of 5 unrelated families clinically diagnosed with hereditary ichthyosis went through WES, followed by extensive segregation analysis. Prenatal diagnosis (PND) was conducted where indicated.

RESULTS

We identified 4 homozygous variants-2 in TGM1 (c.655A > G and c.797A > G) and 2 in ALOX12B (c.527 + 2 T > G and c.1654G > T)-alongside a heterozygous variant in TGM1 (c.428G > A) in 5 families. The variants were all pathogenic/likely pathogenic according to the ACMG classification and segregation analysis, except for c.797A > G in TGM1 which remained a variant of unknown clinical significance. Four variants were novel. All families were referred either during pregnancy or before reproductive planning; 4 benefited from WES as it identified the mutation in the probands and enabled carrier detection in at-risk relatives; PND was conducted in 2 families.

CONCLUSION

Our findings further support WES is a powerful tool for the comprehensive, accurate, and rapid molecular diagnosis of hereditary ichthyosis and can offer opportunities for reproductive planning, carrier screening and prenatal diagnosis to at-risk families.

Histological Evaluation of Products of Conception, Who Benefits from It?

Background: Histopathological evaluation of the first trimester pregnancy loss has always been controversial. Although it is recommended, it is not a part of guidelines.Methods: Six hundred eighty-six samples in a referral infertility clinic were evaluated microscopically and categorized. Two hundred ninety-five cases were evaluated by genetic methods (Multiplex Ligation-dependent Probe Amplification).Results: From 569 samples with chorionic villi, 361 cases had history of three or more abortions. 18.3% of this group showed chronic intervillous of unknown etiology (CIUE) and 8.3% revealed intervilli fibrin deposition, both pathologies with a high risk of recurrence. History of a live child was significantly higher in CIUE group. 29% of genetically evaluated cases had a chromosomal abnormality.Conclusion: Histological evaluation of recurrent pregnancy loss could illuminate the cause of abortion in relatively acceptable percentage of cases, especially in mothers with higher number of previous abortion, mothers with a history of live child and in referral centers.

Molecular characterization of a large cohort of Mucopolysaccharidosis patients: Iran Mucopolysaccharidosis RE-diagnosis Study (IMPRESsion)

Mucopolysaccharidoses (MPSs) are rare, heterogeneous inborn errors of metabolism (IEM) diagnosed through a combination of clinical, biochemical, and genetic investigations. The aim of this study was molecular characterization of the largest cohort of Iranian MPS patients (302 patients from 289 unrelated families), along with tracking their ethnicity and geographical origins. 185/289 patients were studied using an IEM-targeted NGS panel followed by complementary Sanger sequencing, which led to the diagnosis of 154 MPS patients and 5 non-MPS IEMs (diagnostic yield: 85.9%). Furthermore, 106/289 patients who were referred with positive findings went through re-analysis and confirmatory tests which confirmed MPS diagnosis in 104. Among the total of 258 MPS patients, 225 were homozygous, 90 harbored novel variants, and 9 had copy number variations. MPS IV was the most common type (34.8%) followed by MPS I (22.7%) and MPS VI (22.5%). Geographical origin analysis unveiled a pattern of distribution for frequent variants in ARSB (c.430G>A, c.962T>C [p.Leu321Pro], c.281C>A [p.Ser94*]), GALNS (c.319G>A [p.Ala107Thr], c.860C>T [p.Ser287Leu], c.1042A>G [p.Thr348Ala]), and IDUA (c.1A>C [p.Met1Leu], c.1598C>G [p.Pro533Arg], c.1562_1563insC [p.Gly522Argfs*50]). Our extensive patient cohort reveals the genetic and geographic landscape of MPS in Iran, which provides insight into genetic epidemiology of MPS and can facilitate a more cost-effective, time-efficient diagnostic approach based on the region-specific variants. This article is protected by copyright. All rights reserved.

Identification of a novel de novo variant in OTX2 in a patient with congenital microphthalmia using targeted next-generation sequencing followed by prenatal diagnosis

BACKGROUND

Next-generation sequencing has been proven to be a reliable method for the detection of genetic causes in heterogeneous ocular disorders. In this report an NGS-based diagnostic approach was taken to uncover the genetic etiology in a patient with coloboma and microphthalmia, a highly heterogeneous disease with intrafamilial phenotypic variability.

MATERIALS AND METHODS

Next generation sequencing using a targeted panel of 316 genes, was carried out in the proband. Prioritized variants were then identified and confirmed using Sanger sequencing. Prenatal diagnosis of the detected variant was then performed in the family.

RESULTS

A novel de novo frameshift variant c.157_164delTTCACTCG (p.Phe53fs) in OTX2, leading to a truncated protein, was identified. Prenatal diagnosis identified the same variant in the fetus.

CONCLUSIONS

This report demonstrates the importance of genetic counseling and underscores the efficiency and effectiveness of targeted NGS as a means of detecting variants in inherited eye disorders.

Detection of Aneuploidies in Products of Conception and Neonatal Deaths in Iranian Patients Using the Multiplex Ligation-Dependent Probe Amplification (MLPA)

Background:

Around 70% of all pregnancies (Including 15% of clinically-recognized ones) are lost due to various fetal or maternal disorders. Chromosomal aneuploidies are among the most common causes of pregnancy loss. Standard chromosome analysis using G-banding technique (Karyotype) is the technique of choice in studying such abnormalities; however, this technique is time-consuming and sensitive, and limited by vulnerabilities such as cell culture failure. The use of molecular cytogenetic techniques, including array-based techniques and Multiplex Ligation-Dependent Probe Amplification (MLPA), has been proposed to overcome the limitations of this method to study the products of conception. This study has been designed to investigate the feasibility of using MLPA technique as a standalone genetic testing, with histopathologic examinations and genetic counseling to detect aneuploidies in products of conception and neonatal deaths.

Methods:

Forty-two verified fetal and neonatal samples were studies and genetic counseling was scheduled for all parents. Histopathologic examinations were carried out on the products of conception, and appropriate fetal tissues were separated for genetic studies. Following DNA extraction and purification, MLPA was carried out to investigate chromosomal aneuploidies.

Results:

Nine samples (21.42%) were diagnosed to be affected with aneuploidy. Detected aneuploidies were trisomy 22 (n=3), trisomy 21(n=1), trisomy 18 (n=2), trisomy 16 (n=1), trisomy 13 (n=1), and monosomy of chromosome X (n=1). The MLPA analysis results were conclusive for all of the fetal samples (Success rate: 100%).

Conclusion:

These results suggest that MLPA, as a standalone genetic testing, is an accurate, rapid, and reliable method in overcoming the limitations of standard cytogenetic techniques in genetic investigation of products of conception.

Primary ovarian insufficiency with t(5;13): a case report and literature review on disrupted genes

OBJECTIVES

To report a woman with primary ovarian insufficiency (POI) with reciprocal translocation between chromosomes 5 and 13.

METHODS

Chromosomal analysis (G-banding) of a 39-year-old woman with elevated gonadotropin levels and secondary amenorrhea and review of the literature with a special focus on disrupted genes at the reported breakpoints.

RESULTS

A reciprocal translocation between the long arms of chromosomes 5 and 13 was identified in the patient (46,XX,t(5;13)(q13;q14)). Investigation of the breakpoints revealed that the 13q14.1 region encompasses FOXO1 (forkhead box 1) gene, which has an important role in granulosa cell function and follicle maturation.

CONCLUSIONS

Autosomal translocations are rare in women with POI. We have reported the first case of a de novo reciprocal translocation involving chromosomes 5 and 13 in a POI patient. As one of the breakpoints encompasses the FOXO1 gene, it seems that disruption of this gene can be the cause of POI in this patient. This provides further evidence on the role of autosomal translocations in disrupting POI-associated genes. Therefore, concentrating on the genes at the breakpoints will be helpful to delineate the new biological pathways or genes involved in POI pathogenesis.

Prenatal Diagnosis of Tyrosinemia Type 1 Using Next Generation Sequencing

Prenatal diagnosis using conventional molecular genetic techniques may be encountered with some limitations when the disease causing mutation is unknown. Here, we report on prenatal diagnosis of tyrosinemia in a family with consanguineous marriage and two affected children in whom no disease causing mutation had been identified before pregnancy. Mutation analyses of three genes associated with tyrosinemia including FAH, TAT and HPD were carried out in the fetal DNA sample using Next Generation Sequencing. A heterozygous nonsense mutation (p.Arg237Ter) in FAH gene was detected in the fetus. Further investigations suggested that the fetus was carrier of tyrosinemia type 1. This study demonstrates the successful application of Next Generation Sequencing in prenatal diagnosis, when the time is a limiting factor, more than one (especially large) responsible genes are involved, a "founder" or a "previously detected" mutation is not present and hence the conventional molecular genetic investigations cannot be employed.

Experiences of Infertile Women Seeking Assisted Pregnancy in Iran: A Qualitative Study

BACKGROUND

Assisted reproductive technologies (ARTs) are complicated and stressful techniques and the social and cultural norms are major obstacles against their use. Many qualitative studies have been done in the field of women's experiences of infertility, but less is known about the experiences of infertile women seeking assisted pregnancy. The aim of this study was to understand and describe the experience of women who have used assisted reproductive technologies for their current pregnancy.

METHODS

This qualitative study was conducted based on a content analysis approach. With purposive sampling, 12 pregnant women who were using ART were recruited from Avicenna Fertility Center in Tehran. Women were selected purposefully and with maximum variation. Interviews were performed after a positive test of pregnancy and women were introduced to researchers in their first visit of pregnancy in the prenatal clinic. Interviews were recorded, transcribed verbatim and analyzed concurrently. Semi-structured interviews were coded, categorized and the themes were also identified.

RESULTS

Four main themes were uncovered which included struggle to achieve pregnancy, fear and uncertainty, escape from stigma and the pursuit to achieve husband satisfaction.

CONCLUSION

It is essential for these women to be counseled and prepared by their health care providers after the use of ARTs. Distress can be reduced for infertile women seeking assisted pregnancy when they are prepared for possible failures, empowered to deal with stigma, and have their partners' involvement in counseling sessions.

A method for semi-automatic nuchal translucency thickness measurement

Increased nuchal translucency (NT) thickness is associated with major abnormalities of the heart, great arteries and a wide range of genetic syndromes. NT thickness is one of the most important ultrasound markers in fetal diseases screening. To find an applicable method that accurately detects NT, we use an algorithm based on modified level set for semi-automated segmentation of the region. A regression model is used to find the appropriate direction of NT thickness measurement. The results show 4.5% error.

Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies

Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are major causes of blindness. They result from mutations in many genes which has long hampered comprehensive genetic analysis. Recently, targeted next-generation sequencing (NGS) has proven useful to overcome this limitation. To uncover “hidden mutations” such as copy number variations (CNVs) and mutations in non-coding regions, we extended the use of NGS data by quantitative readout for the exons of 55 RP and LCA genes in 126 patients, and by including non-coding 5′ exons. We detected several causative CNVs which were key to the diagnosis in hitherto unsolved constellations, e.g. hemizygous point mutations in consanguineous families, and CNVs complemented apparently monoallelic recessive alleles. Mutations of non-coding exon 1 of EYS revealed its contribution to disease. In view of the high carrier frequency for retinal disease gene mutations in the general population, we considered the overall variant load in each patient to assess if a mutation was causative or reflected accidental carriership in patients with mutations in several genes or with single recessive alleles. For example, truncating mutations in RP1, a gene implicated in both recessive and dominant RP, were causative in biallelic constellations, unrelated to disease when heterozygous on a biallelic mutation background of another gene, or even non-pathogenic if close to the C-terminus. Patients with mutations in several loci were common, but without evidence for di- or oligogenic inheritance. Although the number of targeted genes was low compared to previous studies, the mutation detection rate was highest (70%) which likely results from completeness and depth of coverage, and quantitative data analysis. CNV analysis should routinely be applied in targeted NGS, and mutations in non-coding exons give reason to systematically include 5′-UTRs in disease gene or exome panels. Consideration of all variants is indispensable because even truncating mutations may be misleading.

Heterozygosity assessment of five STR loci located at 5q13 region for preimplantation genetic diagnosis of spinal muscular atrophy

Preimplantation genetic diagnosis (PGD) has been considered as an alternative to prenatal diagnosis for prevention of genetic disorders while avoiding the subsequent termination of pregnancy. However, the limited amount of template DNA available in a single diploid cell used for PGD leads to number of problems including an increased incidence of detectable contamination; amplification failure and allele drop out. Due to their highly polymorphic and amplifiable characteristics, short tandem repeat (STR) analysis has been proposed as a mean to overcome these limitations. Heterozygosity of the applied STRs is of paramount importance in their informativity, and should therefore be studied in any certain population. Here, for the first time, we report on the heterozygosity analysis of five STR markers (D5S1408, D5S1417, D5S610, D5S629 and D5S637) flanking to SMA gene region, to examine their applicability in the PGD for SMA disease. We have also investigated other statistical features of these markers and found that all of the five studied STRs were informative and four meet the Hardy-Weinberg equilibrium for the studied population. Furthermore, our results propose that similar approaches can be used for the PGD of other single gene disorders.

Normal ranges for fetal femur and humerus diaphysis length during the second trimester in an Iranian population

OBJECTIVES

Shortening of the fetal long bones is a sonographic soft marker for screening of Down syndrome in the second trimester that can be influenced by ethnicity. The purpose of this study was to provide normal reference ranges for femur and humerus diaphysis length during the second trimester of pregnancy in an Iranian population.

METHODS

This cross-sectional study was performed on 3011 singleton fetuses at 15 to 28 weeks' menstrual age. The relationship between menstrual age and both femur and humerus diaphysis length was determined, and percentile values for each menstrual week were provided.

RESULTS

The median femur diaphysis length ranged from 18.05 mm at 15 menstrual weeks to 52.20 mm at 28 menstrual weeks, and the mean humerus diaphysis length ranged from 17.65 mm at 15 menstrual weeks to 48.10 mm at 28 menstrual weeks. There was a linear relationship between menstrual age and both femur diaphysis length (R² = 0.957) and humerus diaphysis length (R² = 0.941).

CONCLUSIONS

We have provided normal reference ranges for femur and humerus diaphysis length during the second trimester of pregnancy in an Iranian population.

First-trimester screening for chromosomal abnormalities by integrated application of nuchal translucency, nasal bone, tricuspid regurgitation and ductus venosus flow combined with maternal serum free β-hCG and PAPP-A: a 5-year prospective study

OBJECTIVE

To investigate the performance of first-trimester screening for chromosomal abnormalities by integrated application of nuchal translucency thickness (NT), nasal bone (NB), tricuspid regurgitation (TR) and ductus venosus (DV) flow combined with maternal serum free β-human chorionic gonadotropin (fβ-hCG) and pregnancy-associated plasma protein-A (PAPP-A) at a one-stop clinic for assessment of risk (OSCAR).

METHODS

In total, 13,706 fetuses in 13,437 pregnancies were screened for chromosomal abnormalities during a period of 5 years. Maternal serum biochemical markers and maternal age were evaluated in combination with NT, NT + NB, NT + NB + TR, and NT + NB + TR + DV flow data in 8581, 242, 236 and 4647 fetuses, respectively.

RESULTS

In total, 51 chromosomal abnormalities were identified in the study population, including 33 cases of trisomy 21, eight of trisomy 18, six of sex chromosome abnormality, one of triploidy and three of other unbalanced abnormalities. The detection rate and false-positive rate (FPR) for trisomy 21 were 93.8% and 4.84%, respectively, using biochemical markers and NT, and 100% and 3.4%, respectively, using biochemical markers, NT, NB, TR and DV flow.

CONCLUSION

While risk assessment using combined biochemical markers and NT measurement has an acceptable screening performance, it can be improved by the integrated evaluation of secondary ultrasound markers of NB, TR and DV flow. This enhanced approach would decrease the FPR from 4.8 % to 3.4 %, leading to a lower number of unnecessary invasive diagnostic tests and subsequent complications, while maintaining the maximum level of detection rate. Pre- and post-test genetic counseling is of paramount importance in either approach.

Her2 amplification status in Iranian breast cancer patients: comparison of immunohistochemistry (IHC) and fluorescence in situ hybridisation (FISH)

INTRODUCTION

Her2/neu is a biomarker which is amplified and/or overexpressed in a subset of breast cancer patients who are eligible to receive trastuzumab. Her-2 gene amplification analysed by fluorescence in situ hybridisation (FISH) and/or protein over-expression detected by immunohistochemistry (IHC) are the two main methods used to detect Her-2 status in clinical practice. The concordance rate between the two techniques is controversial.

METHODS

FISH analysis were performed on 104 tumoural samples from breast cancer patients with known IHC results to determine the Her2 gene status. The FISH/IHC analyses results were then compared and the concordance rate was determined.

RESULTS

Her2 gene amplification was detected in 0 of IHC score 1+, 24/86 (27.91%) 2+, and 8/13 (61.54%) 3+. The IHC and FISH results concordance rates were 100%, 27.9%, and 61.5% for IHC scores of 1+, 2+, and 3+ respectively.

CONCLUSION

The results of this study suggest that IHC 1+ should be considered as negative while IHC 2+ results need further confirmative analysis by FISH. Further quality control and standardization of IHC technique are required to improve the concordance rate between the two methods.

Molecular cytogenetic analysis of urothelial carcinomas using urine samples

Urinary cells obtained from voided urine specimens of 46 patients with urothelial carcinomas (UCs) and 10 normal individuals were analyzed with 3 different centromeric fluorescence in situ hybridization (FISH) probes. The overall sensitivity of cytology was 48.9% compared to 95.7%with the FISH technique. The minimum values were found for stage Ta and grade 1 (90.5 and 89.4) and sensitivity of FISH in other stages and grades was 100%. Chromosome 3 demonstrated the most frequent chromosomal abnormality in all samples (43%), followed by chromosome 17 (32%) and chromosome 7 (25%). There was a statistically significant association between the number of cell abnormalities in chromosome 17 and the tumour stage (p value=0.02). No relationship was found between the type of chromosomal abnormality and grade. Thus feasibility and reliability of a FISH based approach was confirmed for detection of UC in urine samples.

Chromosomal radiosensitivity in patients with common variable immunodeficiency

Common variable immunodeficiency (CVID) is a heterogeneous group of primary immunodeficiency disorders. In addition to recurrent infections and autoimmunity, cancers are more prevalent in these patients than the normal population. Increased radiosensitivity may be a reason for the increased malignancies. To analyze chromosomal radiosensitivity of CVID patients, lymphocytes were cultured from 20 CVID patients. After irradiation (50, 100 cGy), metaphases were evaluated for chromosomal aberrations. Results were compared in patients, healthy individuals, and ataxia telangiectasia as positive controls. Before irradiation there was no difference between groups of patients, but after radiation, the incidence of all kinds of aberrations was higher in the CVID patients and this was statistically significant at 100 cGy (P<0.05). CVID patients appear to be susceptible to in vitro irradiation. These patients should be protected from unnecessary radiographic diagnostic and therapeutic procedures. Also, radiosensitivity may help classifying CVID patients.

Prevalence of human papillomavirus genotypes in women with normal and abnormal cervical cytology in Iran

INTRODUCTION

HPV infection has a prime etiologic role in development and progression of cervical cancer, one of the most frequent forms of cancer among women in developing countries. This study was designed to determine the most prevalent HPV genotypes in women with normal and abnormal cervical cytology in Iran.

MATERIALS AND METHODS

Samples from134 patients, including 127 who attended gynecology clinics and 7 with solid cervical tumors were used. All 127 patients underwent routine Pap tests for cytological evaluation and at the same visit a sample of cervical epithelial cells was obtained by scraping the cervix osteum. In each case HPV infection was primarily evaluated by PCR using GP 5/6 primers and then subtyping was performed in proved infected samples with specific primers for HPV 16, 18, 31, 33, 11 and 6. After cytological evaluation, 50 patients with abnormal Pap tests were categorized as the abnormal group and the remaining 77 patients as the normal group.

RESULTS

In the normal group, HPV infection was established in 10 cases (13% infection rate), while 30 HPV positive cases were discovered in the abnormal group (60% infected). The most prevalent genotypes among the infected samples were HPV 16 (76%), HPV18 (12.7%) and HPV11/6 (8.5%). Moreover, all 7 tumor samples were positive for HPV general primers of which, 5 samples were infected with HPV 16, two were co-infected with HPV16,18 and HPV16,31 genotypes and one was infected with HPV 18.

CONCLUSIONS

Infection with HPV 16 was found to be significantly higher in abnormal group in comparison with normal group (42% vs. 11.6%, P value <0.005), likewise HPV18 genotypes were proved to be more prevalent in abnormal group (8% vs. 0%, P value <0.05). No significant relation between other HPV genotypes and pathologic cervical changes was obtained. According to our study high rates of infection with HPV genotypes in sexually active Iranian women makes molecular investigation for HPV16 and 18 very essential in clinical approaches to patients with proven dysplasia in their screening tests and also for those patients with borderline (i.e. ASCUS) or incongruous pathology reports. Larger studies are required to determine the most appropriate vaccine with highest protection in Iranian women.

Mosaic supernumerary ring chromosome 19 identified by comparative genomic hybridisation

We report the use of comparative genomic hybridisation (CGH) to define the origin of a supernumerary ring chromosome which conventional cytogenetic banding and fluorescence in situ hybridisation (FISH) methods had failed to identify. Targeted FISH using whole chromosome 19 library arm and site specific probes then confirmed the CGH results. This study shows the feasibility of using CGH for the identification of supernumerary marker chromosomes, even in fewer than 50% of cells, where no clinical or cytogenetic clues are present.

A new strategy for cryptic telomeric translocation screening in patients with idiopathic mental retardation

Cryptic unbalanced chromosome rearrangements in the telomeric bands of human chromosomes constitute a significant cause of "idiopathic" mental retardation. Here, we have described a new strategy based upon comparative genomic hybridisation (CGH) to screen for these abnormalities. A modified CGH analysis showed three unbalanced cryptic rearrangements in five patients from three families. These chromosome abnormalities and their balanced forms in the relatives were then confirmed by fluorescence in situ hybridisation (FISH). This study describes a new approach to the diagnosis of cryptic translocations between the G band negative ends of chromosomes and confirms the significant contribution of cryptic telomeric rearrangements to idiopathic mental retardation.