Frequent copy number variants in a cohort of Mexican-Mestizo individuals.

BACKGROUND: The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals. RESULTS: In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared. CONCLUSION: The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.

Inherited bone marrow failure syndromes: phenotype as a tool for early diagnostic suspicion at a major reference center in Mexico.

Introduction: The inherited bone marrow failure syndromes (IBMFSs) are a group of rare disorders characterized by bone marrow failure (BMF), physical abnormalities, and an increased risk of neoplasia. The National Institute of Pediatrics (INP) is a major medical institution in Mexico, where patients with BMF receive a complete approach that includes paraclinical tests. Readily recognizable features, such as the hematological and distinctive physical phenotypes, identified by clinical dysmorphologists, remain crucial for the diagnosis and management of these patients, particularly in circumstances where next-generation sequencing (NGS) is not easily available. Here, we describe a group of Mexican patients with a high clinical suspicion of an IBMFS. Methods: We performed a systematic retrospective analysis of the medical records of patients who had a high IBMFS suspicion at our institution from January 2018 to July 2021. An initial assessment included first ruling out acquired causes of BMF by the Hematology Department and referral of the patient to the Department of Human Genetics for physical examination to search for specific phenotypes suggesting an IBMFS. Patients with high suspicion of having an IBMFS were classified into two main groups: 1) specific IBMFS, including dyskeratosis congenita (DC), Diamond-Blackfan anemia (DBA), Shwachman-Diamond syndrome (SDS), thrombocytopenia with absent radii (TAR), and severe congenital neutropenia (SCN); 2) undefined IBMFS (UI). Results: We established a high suspicion of having an IBMFS in 48 patients. At initial evaluation, the most common hematologic features were bicytopenia (20%) and aplastic anemia (16%); three patients received hematopoietic stem cell transplantation. Among patients with a suspicion of an IBMFS, the most common physical abnormality was minor craniofacial features in 83% of patients and neurodevelopmental disorders in 52%. The specific suspicions that we built were DBA (31%), SDS (18%), DC (14%), TAR (4%), and SCN (4%), whereas 27% of cases remained as undefined IBMFS. SDS, TAR, and SCN were more commonly suspected at an earlier age (<1 year), followed by DBA (2 years) and DC (5 years). Conclusions: Thorough examination of reported clinical data allowed us to highly suspect a specific IBMFS in approximately 70% of patients; however, an important number of patients remained with suspicion of an undefined IBMFS. Implementation of NGS and telomere length measurement are forthcoming measures to improve IBMFS diagnosis in Mexico.

Non-classical 1p36 deletion in a patient with Duane retraction syndrome: case report and literature review.

BACKGROUND: Monosomy of 1p36 is considered the most common terminal microdeletion syndrome. It is characterized by intellectual disability, growth retardation, seizures, congenital anomalies, and distinctive facial features that are absent when the deletion is proximal, beyond the 1p36.32 region. In patients with proximal deletions, little is known about the associated phenotype, since only a few cases have been reported in the literature. Ocular manifestations in patients with classical 1p36 monosomy are frequent and include strabismus, myopia, hypermetropia, and nystagmus. However, as of today only one patient with 1p36 deletion and Duane retraction syndrome (DRS) has been reported. CASE PRESENTATION: We describe a patient with intellectual disability, facial dysmorphism, and bilateral Duane retraction syndrome (DRS) type 1. Array CGH showed a 7.2 Mb de novo deletion from 1p36.31 to 1p36.21. DISCUSSION: Our patient displayed DRS, which is not part of the classical phenotype and is not a common clinical feature in 1p36 deletion syndrome; we hypothesized that this could be associated with the overlapping deletion between the distal and proximal 1p36 regions. DRS is one of the Congenital Cranial Dysinnervation Disorders, and a genetic basis for the syndrome has been extensively reported. The HES3 gene is located at 1p36.31 and could be associated with oculomotor alterations, including DRS, since this gene is involved in the development of the 3rd cranial nerve and the 6th cranial nerve's nucleus. We propose that oculomotor anomalies, including DRS, could be related to proximal 1p36 deletion, warranting a detailed ophthalmologic evaluation of these patients.

Derivative chromosomes involving 5p large rearranged segments went unnoticed with the use of conventional cytogenetics.

BACKGROUND: In countries where comparative genomic hybridization arrays (aCGH) and next generation sequencing are not widely available due to accessibility and economic constraints, conventional 400-500-band karyotyping is the first-line choice for the etiological diagnosis of patients with congenital malformations and intellectual disability. Conventional karyotype analysis can rule out chromosomal alterations greater than 10 Mb. However, some large structural abnormalities, such as derivative chromosomes, may go undetected when the analysis is performed at less than a 550-band resolution and the size and banding pattern of the interchanged segments are similar. Derivatives frequently originate from inter-chromosomal exchanges and sometimes are inherited from a parent who carries a reciprocal translocation. CASE PRESENTATION: We present two cases with derivative chromosomes involving a 9.1 Mb 5p deletion/14.8 Mb 10p duplication in the first patient and a 19.9 Mb 5p deletion/ 18.5 Mb 9p duplication in the second patient. These long chromosomal imbalances were ascertained by aCGH but not by conventional cytogenetics. Both patients presented with a deletion of the Cri du chat syndrome region and a duplication of another genomic region. Each patient had a unique clinical picture, and although they presented some features of Cri du chat syndrome, the phenotype did not conclusively point towards this diagnosis, although a chromosomopathy was suspected. CONCLUSIONS: These cases highlight the fundamental role of the clinical suspicion in guiding the approach for the etiological diagnosis of patients. Molecular cytogenetics techniques, such as aCGH, should be considered when the clinician suspects the presence of a chromosomal imbalance in spite of a normal karyotype.

Further delineation of achondroplasia-hypochondroplasia complex with long-term survival.

Achondroplasia-hypochondroplasia (ACH-HCH) complex is caused by the presence of two different pathogenic variants in each allele of FGFR3 gene. Only four patients with confirmed molecular diagnoses have been reported to date, and the phenotype has not been fully defined. Here, we describe a Mexican patient with a confirmed molecular diagnosis of ACH-HCH complex. This patient exhibits intellectual disability, has a history of seizures, experienced multiple cardiorespiratory complications during early childhood, and required foramen magnum decompression. However, he now shows a stable health condition with long-term survival (current age, 18 years). This case is particularly relevant to our understanding of ACH-HCH complex and for the genetic counseling of couples who are affected with ACH or HCH.

7p15 deletion as the cause of hand-foot-genital syndrome: a case report, literature review and proposal of a minimum region for this phenotype.

BACKGROUND: Hand-foot-genital syndrome (HFGS) is a rare condition characterized by congenital malformations in the limbs and genitourinary tract. Generally, this syndrome occurs due to point mutations that cause loss of function of the HOXA13 gene, which is located on 7p15; however, there are some patients with HFGS caused by interstitial deletions in this region. CASE PRESENTATION: We describe a pediatric Mexican patient who came to the Medical Genetics Department at the National Institute of Pediatrics because he presented with genital, hand and feet anomalies, facial dysmorphisms, and learning difficulties. Array CGH reported a 12.7 Mb deletion that includes HOXA13. CONCLUSIONS: We compared our patient with cases of HFGS reported in the literature caused by a microdeletion; we found a minimum shared region in 7p15.2. By analyzing the phenotype in these patients, we suggest that microdeletions in this region should be investigated in all patients with clinical characteristics of HFGS who also present with dysplastic ears, mainly low-set implantation with a prominent antihelix, as well as a low nasal bridge and long philtrum.

Setleis syndrome in Mexican-Nahua sibs due to a homozygous TWIST2 frameshift mutation and partial expression in heterozygotes: review of the focal facial dermal dysplasias and subtype reclassification.

BACKGROUND: The focal facial dermal dysplasias (FFDDs) are a group of inherited disorders of facial development, characterised by bitemporal or preauricular scar-like defects, the former resembling 'forceps marks'. Recently, different homozygous TWIST2 nonsense mutations were reported in unrelated Setleis syndrome (FFDD Type III) patients from consanguineous families, consistent with autosomal recessive inheritance. Mexican-Nahua sibs with facial and ophthalmologic features of FFDD type III were evaluated. METHODS: Genomic DNAs were isolated for sequencing of the TWIST2 gene. The clinical features and inheritance of all previously reported FFDD patients were reviewed. RESULTS: The affected sibs were homozygous for a novel TWIST2 frameshift mutation, c.168delC (p.S57AfsX45). Notably, both parents and two heterozygous sibs had distichiasis and partial absence of lower eyelashes. The FFDD subtypes were reclassified: the 'Brauer-Setleis' phenotype (autosomal dominant with variable expressivity) as FFDD type II; and patients with preauricular lesions as a new subtype, FFDD type IV. CONCLUSIONS: FFDD type III heterozygotes with TWIST2 mutations may have syndromic manifestations. Review of previous FFDD patients resulted in reclassification of the subtypes.

Detection of short-term chromosomal damage due to therapeutic 131I exposure in patients with thyroid cancer.

We evaluated the chromosomal aberration (CA) frequencies in the peripheral blood lymphocytes of ten female patients, age average 43.7 +/- 12.9, with thyroid cancer (TC) who had been exposed to 100-200 mCi therapeutic doses of 131I. The blood samples were obtained before-treatment and at 2 and 24 h after-treatment. Radiation was measured in the samples by means of dysprosium-activated calcium sulfate thermoluminescent dosimetry. The maximum radiation levels were detected in the samples taken 2 h after treatment. A positive correlation was found between the sample-emitted radiation values and the frequencies of CAs (r = 0.495; p < 0.01). The average baseline frequency of aberrations found in the ten studied patients was 0.009 per cell. Upon application of the 131I therapeutic dose, this frequency increased to 0.04 and 0.02 CAs/cell at 2 and 24 h after-treatment, respectively (p < 0.05). Break-type aberrations experienced a peak at 2 h after-treatment, whereas rejoined aberrations, such as dicentrics, rings, and radial figures, increased with sampling time. Seven patients with metastases had high amounts of CAs at 2 and 24 h after-treatment, in comparison to three patients without metastases who had a lower frequency of CAs at 24h aftertreatment. This difference could be due to the fact that circulating lymphocytes were exposed to a greater cancerous tissue mass, which retains 131I during the diagnostic and therapeutic processes. These results demonstrate the importance of detecting and surgically removing the largest possible amount of thyroid tissue in order to diminish the exposure of normal cells to radiation.

Acrocentric cryptic translocation associated with nondisjunction of chromosome 21.

Down syndrome is the most frequent autosome aneuploidy in live newborns. It was recently proposed that pericentromeric cryptic translocations might be a cause of chromosome nondisjunction. We describe here a phenotypically normal subject with a cryptic translocation involving the short arms of chromosomes 13 or 21 and 22, who had a son with Down syndrome. Fluorescent in situ hybridization (FISH) on paternal metaphase chromosomes showed a chromosome 22 centromere positive for both 13/21 and 14/22 centromeric probes. The same probes hybridized on different and contiguous sites of chromatin fibers, eliminating cross-hybridization artifacts. This confirmed the presence of a cryptic translocation generating a dicentric chromosome 22: fib ish dic(21;22)(21 pter --> 21q10::22q10 --> 22 qter)(D13/21Z1+;D14/22Z1+). Microsatellite STR segregation analysis confirmed the paternal origin of the additional chromosome 21 in the Down syndrome patient. To determine whether the father showed a higher-than-normal frequency of chromosome 21 nondisjunction, FISH analysis of spermatozoa was performed using a sequence specific probe (21q22.13-q22.2). The frequency of disomy 21 spermatozoa was twofold higher in the cryptic translocation carrier as compared to normal subjects (P < 0.014), suggesting that the rearrangement favored the nondisjunction of chromosome 21. This is the first report associating a pericentromeric cryptic translocation of acrocentric chromosomes with the generation of aneuploidy, supporting the hypothesis that this type of rearrangement may contribute to abnormal chromosomal segregation.

Patient follow-up is a major problem at genetics clinics.

Children with genetic diseases must be followed for long periods of time to seek new findings. Other patients require further check-ups and studies to be diagnosed. Some patients never return for medical care after the first consultation, which may have serious consequences. We reviewed 400 medical charts of patients with genetic disease to analyze overall attendance to the genetics clinic, investigate some of the causes of failure to seek medical advice, and determine the differences between those first seen as outpatients or as inpatients. The mean follow-up period was 8.3 months (range 0-79), and the average number of visits was 2.8 (range 1-16). Forty eight percent of the cases first seen as inpatients were evaluated only once and 14% twice; while 22 and 21% of the 300 cases first seen as outpatients attended once and twice, respectively (P = 0.0). Appointment keeping was apparently not affected by the presence or absence of diagnosis. Overall, 97 patients were discharged, 7 died, 55 continued on follow-up, 62 attended other hospital services-but not genetics-and 179 were completely lost to follow-up. Diagnosed patients were counseled more frequently than undiagnosed patients (62 vs. 5%); and 71% of the diagnosed patients first seen as outpatients but only 36% of undiagnosed cases first seen as inpatients were counseled, differences between these two groups were significant (P = 0.005). We conclude that keeping the patient with genetic disease on follow-up is a difficult task. New educational strategies must be planned to improve this worrisome situation.

Detection of mosaicism in lymphocytes of parents of free trisomy 21 offspring.

Down syndrome (DS) resulting from free trisomy 21 (FT21) has been largely associated with advanced maternal age. However, approximately 60% of FT21 cases are born to young couples. Thus, the etiological factors responsible for these FT21 children must differ from those proposed for maternal age-related FT21. These factors have not been defined. In this study, we analyzed the chromosomes of peripheral blood lymphocytes from three groups of couples aged < or =35 years, to identify chromosomal trisomies: Group I included 5 couples with normal offspring; Group II included 22 couples with one FT21 child; and Group III consisted of 3 couples with recurrent FT21. A total of 13,809 metaphases were analyzed with G-banding and 60,205 metaphases were analyzed with FISH using a 13/21 centromeric probe. Aneuploidy was significantly more frequent in Groups II and III. The frequencies of hyperdiploid cells were 0.19, 0.49 and 0.96% in Groups I-III, respectively. FISH analysis showed that trisomy 21 cell percentages were 0.08, 0.21 and 0.76 for Groups I-III, respectively, and were very similar to those obtained with G-banding. Trisomy 21 mosaicism was found in 2/22 couples with one FT21 offspring, and in 2/3 couples with recurrent FT21. Our data suggest that mosaicism is an important cause of FT21 offspring in young couples, and that aneuploidy is more frequent among couples with FT21 offspring. This may be related with age and other undetermined intrinsic and extrinsic factors.

Displasia mandíbulo acral en un paciente pediátrico mexicano / Mandibulo acral dysplasia in a Mexican children

Introducción. La displasia mandíbulo acral (DMA) es una rara enfermedad autosómica recesiva, originalmente descrita en 1917. A la fecha se han descrito aproximadamente 20 casos, de los cuales la mayoría son de origen italiano. Caso clínico. Se presenta al primer paciente pediátrico mexicano comparando los hallazgos clínicos y radiológicos de este caso con los encontrados en la literatura y con las entidades que deben considerarse en el diagnóstico diferencial tales como: progeria, acrogeria, displasia cleidocraneal, picnodisostosis, Hallerman-Streiff, Hadju-Cheney síndrome de Werner. Conclusiones. Aunque la DMA tiene una frecuencia baja, en la práctica debe considerarse esta entidad en aquellos pacientes con hipoplasia mandibular o alteraciones dermatológicas como hiperpigmentación moteada

Microtia: A clinical and genetic study at the National Institute of Pediatrics in Mexico City

Background. Microtia is a malformation of the ear with extreme variability of expression. It is generally seean as an isolated malformation. However, some authors consider it to be a minimal manifestation of the oculo-auriculo-vertebral spectrum (OAVS), wherem, in addition, there are facial, vertebral, and renal abnormalities, among others. Methods. A total of 145 pediatric patients with unilateral or bilateral microtia not considered as part of a syndrome were studied. All patients were subjected to an international clinical examination, a familial history, and radiographic imaging studies for ruling out associated malformations. Patients were classified into two groups: group 1 (60 percent), with isolated microtia; and group 2 (40 percent), considered as OAVS, with microtia associated with hemifacial skeletal microsomia, vertebral and/or renal malformations. Results. No significant differences were found between the groups when the following variables were compared: gender; prescence of unilateral or bilateral microtia; atretic external auditory canal; presence of preauricelar tags; hearing loss of any type, and affection of the seventh cranial nerve, as well as associated malformations of other otgans or systems. There were significant differences in relation to the presence of soft-tissue hemifacial microsomia, more frequently seen in patients with OAVS, because the majority of these patients had bone microsomia. Over 66 percent of the cases were sporadic and the rest were familiar. In 28.3 percent of the cases, the history suggested an autosomal-dominant inheritance pattern, and in 5.5 percent, an autosomal-recessive inheritance pattent, although in some familial cases, multifactorial inheritance could not be ignored . Some members in several familes has isolated microtia, and others had mild characteristic manifestations of OAVS. Conclusions. Our results support the hypothesis that isolated microtia is a minimal expression of OAVS. Therefore, it is recommended that patients with microtia be subjected to intentional studies that search for malformations and physical examinations of firstdegree relatives for adquate genetic counseling and management

Detección de aneuploidías por hibridación in situ en células de mucosa oral / Detection of aneuploides in bucal mucosa by in situ hibridization

La técnica de hibridación in situ con fluorescencia (FISH) permite identificar alteraciones cromosómicas sin necesidad de cultivo en células en interfase. En este trabajo se realizó el estudio de FISH en 15 pacientes con diagnóstico citogenético de trisomía 21 regular, cinco pacientes cuyo estudio citogenético en sangre había mostrado la presencia de mosaicismo, y uno en el cual se identificó un cromosoma marcador sin evidencia de mosaicismo. Cinco sujetos con cariotipo normal sirvieron como testigo. De cada paciente se obtuvieron células de descamación de la mucosa oral; para facilitar la penetración de la sonda, se hizo pretratamiento mediante digestión con pepsina durante 20 minutos. En los 15 pacientes con síndrome de Down, la técnica de FISH con sonda Ó-satélite 13/21 mostró, en todas las células, cinco señales fluorescentes de las cuales tres correspondía al cromosoma 21 y dos al cromosoma 13, mientras que en los normales hubo cuatro señales. En un caso con fenotipo de síndrome de Turner, el estudio citogenético en 50 metafases había mostrado un cariotipo 46,X+mar mientras que el análisis de 1000 núcleos con la técnica de FISH permitió reconocer que el cromosoma maracador provenía de un cromosoma X y la presencia de un mosaicismo 45,X/46,X,r(X). En los otros casos de mosaicismo, el porcentaje de células con FISH pero estas diferencias no fueron significativas. En conclusión, el método de FISH en células de la mucosa bucal proporcionó resultaos confiables y al ser rápido y no invasivo, puede utilizarse para el diagnóstico de aberraciones cromosómicas, principalmente cuando se dificulta el estudio citogenético en sangre periférica

Identificación de cromosomas sexuales marcadores mediante hibridación in situ con fluorescencia (FISH) / Identification of sex chomosome markers using fluorescence in situ hybridization (FISH)

Del 6 al 15 de los casos son síndrome de Turner presentan un cariotipo en mosaico con una línea 45,X, y otra con un pequeño cromosoma sexual marcador de origen no determinado, que puede ser un anillo o un fragmento céntrico. La identificación de su origen, que frecuentemente se dificulta por la falta de resolución de las técnicas citogenéticas y la variabilidad en el fenotipo clínico , es de vital importancia ya que, si provienen de un cromosoma Y, el paciente tiene un riesgo elevado de desarrollar gonadoblastoma. El objetivo del presente trabajo fue determinar el origen de pequeños cromosomas sexuales marcadores mediante la técnica de hibridación in situ con fluorescencia (FISH). Se estudiaron ocho pacientes: siete mostraban fenotipo Turner con genitales externos femeninos, y la octava tenía talla baja con ambigüedad de genitales. En todos los casos se identificó, en el cariotipo de sangre periférica, un mosaico con una línea celular que presentaba un cromosoma sexual marcador; en tres se corroboró el mosaico en fibroblastos. Para la técnica de FISH se utilizaron sondas de DNA marcadas con biotina, con secuencias complementarias a la región centroamérica alfa satélite de los cromosomas X y Y. Con la sonda alfa satélite del X, se estableció que el cromosoma marcador provenía del X en siete pacientes. En la paciente con genitales ambiguos, se determinó que el marcador derivaba del cromosoma Y. Consecuentemenete la técnica FISH fue capaz de identificar el origen de los cromosomas sexuales marcadores en las ocho pacientes

Ambigüedad de genitales I. Abordaje inicial del paciente / Ambigous genitalia. Initial diagnosis approach

Se presentan los criterios para el abordaje diagnóstico inicial de pacientes con alteraciones en la diferenciación sexual, de acuerdo a los lineamientos del Grupo Para el Estudio del Intersexo del Instituto Nacional de Pediatría. Una vez definidas las alteraciones genitales de cada paciente, así como sus antecedentes personales y familiares, se sugiere un protocolo de exámenes paraclínicos indispensables para iniciar el abordaje sindromático. Se hace énfasis en la necesidad de no establecer una asignación sexual social ni funcional hasta no haber esclarecido la etiología precisa del trastorno.

Estudio de heterogeneidad genética en anemia de Fanconi por medio de la adición del plasma / Genetic heterogenicity study in Fanconis anemia by the addition of plasma

Con el objetivo de investigar heterogeneidad genética en la variedad infantil de anemia de Fanconi (AF) se realizaron cultivos de linfocitos de pacientes con Af con plasma autólogo, con plasma de otros pacientes con AF y con plasma normal. Se sembraron además linfocitos de un sujeto normal con plasma autólogo y con plasma de cada uno de los pacientes con AF. Para cada tipo de cultivo se cuantificó la freuencia de aberraciones cromossómicas inducidas por MMC. Los linfocitos de pacientes con AF cultivados con plasma autólogo mostraron hipersensibilidad a la MMC y una disminución significativa de la frecuencia de aberraciones inducidas en los cultivos con plasma normal. Sin embargo, en presencia del plasma de los otros pacientes la gran variabilidad en la respuesta de los linfocitos de los pacientes con AF a la MMC no permitió demostrar heterogeneidad genética. Esto pudiera deberse a que a pesar de existir heterogeneidad genética la metodología empleada no pudiera evidenciarla o bien, a que nuestros pacientes correspondiean ala mismo tipo de AF