Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology.

Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.

Fístula pancreática: una complicación temida. Experiencia en una unidad de cirugía hepatobiliopancreática de cuarto nivel / Pancreatic fistula: A feared complication. Experience in a fourth level hepatobiliopancreatic surgery unit

Introducción. La fístula pancreática postoperatoria es una de las complicaciones más importantes en la cirugía hepatobiliopancreática. Su diagnóstico se hace mediante la presencia de un nivel de amilasa en el líquido de drenaje al menos tres veces por encima del valor de la amilasa en suero a partir del tercer día postoperatorio. El objetivo de este estudio fue caracterizar los pacientes con fístula pancreática postoperatoria en nuestra institución, evaluando la importancia de la detección temprana y el establecimiento de un manejo oportuno. Métodos. Estudio descriptivo, retrospectivo, que incluyó los pacientes sometidos a pancreatoduodenectomía, con diagnóstico de fístula pancreática postoperatoria como complicación de cirugía hepatobiliopancreática, en el Hospital Internacional de Colombia, en Piedecuesta, entre enero del 2017 y diciembre de 2020. Se excluyeron los pacientes con otro tipo procedimiento quirúrgico y aquellos que decidieron no participar en el estudio. Resultados. Se evaluaron 69 pacientes, con un predominio del sexo femenino (n=38; 55,1 %) y mediana de la edad de 57 años. El 33,3 % (n=24) de los pacientes intervenidos desarrollaron fístula pancreática postoperatoria, siendo el 23,2 % fuga bioquímica, grado B 8,7 % y grado C 2,9 %, para quienes se indicaron manejo expectante, control ecográfico y reintervención, respectivamente. Fallecieron 5 pacientes (7,2 %). Conclusiones. La fístula pancreáticapostoperatoria es una complicación para tener en cuenta en todos los pacientes sometidos a pancreatoduodenectomía. Existen estrategias que pueden permitir disminuir la incidencia de esta complicación, con el fin de mejorar el desenlace, el pronóstico y la morbilidad posquirúrgica.

Introduction. Postoperative pancreatic fistula is one of the most important complications in hepatobiliopancreatic surgery. Its diagnosis is made by the presence of an amylase level in the drainage fluid at least three times above the serum amylase value from the third postoperative day. The objective of this study was to characterize patients with postoperative pancreatic fistula at our institution, evaluating the importance of early detection and to establish a timely management. Methods. Descriptive, retrospective study that included patients who underwent pancreatoduodenectomy with a diagnosis of postoperative pancreatic fistula as a complication of hepatobiliopancreatic surgery at the Hospital Internacional Colombia, between January 2017 and December 2020. Patients with another type of procedure performed by this specialty and those who did not decide to participate in the study were excluded. Results. A total of 69 patients were included, the median age was 57 years with a predominance of females (n=38; 55.1%). 33.3% (n=24) of the operated patients developed postoperative pancreatic fistula, with 23.2% having a biochemical leak, grade B in 8.7% and grade C in 2.9%, for whom expectant management, ultrasound control and reintervention were indicated, respectively. Five patients died (7.2%). Conclusions. Pancreatic fistula is a complication to take into account in all patients undergoing pancreatoduodenectomy. There are strategies that can reduce the incidence of this complication and thus improve not only the outcome but also the prognosis and postoperative morbidity.

Shallow whole-genome sequencing of bone marrow aspirates in myelodysplastic neoplasms: A retrospective comparison with cytogenetics.

Copy number alterations (CNA) are powerful prognostic markers in myelodysplastic neoplasms (MDS) and are routinely analyzed by conventional cytogenetic analysis (CCA) on bone marrow (BM). Although CCA is still the gold standard, it requires extensive hands-on time and highly trained staff for the analysis, making it a laborious technique. To reduce turn-around-time per case, shallow whole genome sequencing (sWGS) technologies offer new perspectives for the diagnostic work-up of this disorder. We compared sWGS with CCA for the detection of CNAs in 33 retrospective BM samples of patients with MDS. Using sWGS, CNAs were detected in all cases and additionally allowed the analysis of three cases for which CCA failed. The prognostic stratification (IPSS-R score) of 27 out of 30 patients was the same with both techniques. In the remaining cases, discrepancies were caused by the presence of balanced translocations escaping sWGS detection in two cases, a subclonal aberration reported with CCA that could not be confirmed by FISH or sWGS, and the presence of an isodicentric chromosome idic(17)(p11) missed by CCA. Since sWGS can almost entirely be automated, our findings indicate that sWGS is valuable in a routine setting validating it as a cost-efficient tool.

Alteraciones cardíacas en los pacientes con enfermedad tiroidea / Cardiac disorders in patients with thyroid disease

Resumen Introducción: Al hablar de los trastornos funcionales de la glándula tiroides se hace referencia al aumento o la disminución en la producción de hormonas tiroideas; estos reciben el nombre de hipertiroidismo e hipotiroidismo, respectivamente. Son condiciones que han sido ampliamente estudiadas por el impacto negativo que tienen en el organismo, ya que ocasionan cambios en el metabolismo y generan alteraciones que llevan a que el paciente presente una serie de complicaciones graves, como son las enfermedades cardíacas. Objetivo: Identificar las alteraciones cardíacas en pacientes con enfermedad tiroidea. Método: Se realizó una revisión sistemática de las publicaciones disponibles en las bases de datos que hacen referencia a la enfermedad tiroidea y su relación con las alteraciones en el corazón. Resultados: En total se incluyeron 35 artículos publicados en los últimos 10 años, en distintos idiomas, en los que se evaluaba la asociación entre la enfermedad tiroidea y las alteraciones cardíacas. Conclusiones: Las enfermedades tiroideas están íntimamente relacionadas con cardiopatías que pueden empeorar la gravedad del cuadro clínico del paciente, e incluso asociarse con un incremento en la mortalidad de los mismos. Algunas de las cardiopatías mencionadas son cambios valvulares mixomatosos, disfunción endotelial, miocarditis, pericarditis aguda, vasoespasmo coronario, fibrilación atrial en el caso del hipertiroidismo, fibrosis endocárdica, aumento de la rigidez miocárdica, pericarditis, derrame pericárdico, estenosis coronaria y bradicardia sinusal por efecto del hipotiroidismo.

Abstract Introduction: When speaking of functional disorders of the thyroid gland, reference is made to increased or decreased production of thyroid hormones. These were called hyperthyroidism and hypothyroidism respectively. They are pathologies that have been studied for the negative impact they have on the body, since they cause changes in the metabolism; thus generating alterations that lead to the patient presenting a series of serious complications, such as cardiac pathologies. Objective: To identify cardiac disorders in patients with thyroid disease. Method: A systematic review of the publications available in the databases that refer to thyroid pathology and its relationship with heart level disorders was performed. Results: A total of 35 articles published in the last 10 years, in different languages, which evaluate the association between thyroid pathology and cardiac abnormalities are included. Conclusions: Thyroid pathologies are closely related to heart disease that can worsen the severity of the patient’s clinical condition, and may even be associated with an increase in their mortality. Some of the mentioned heart diseases are: myxomatous valve changes, endothelial dysfunction, myocarditis, acute pericarditis, coronary vasospasm, atrial fibrillation in the case of hyperthyroidism; endocardial fibrosis, increased myocardial rigidity, pericarditis, pericardial effusion, coronary stenosis, and sinus bradycardia due to hypothyroidism.

Ultra-low coverage whole genome sequencing of ccfDNA in multiple myeloma: A tool for laboratory routine?

Multiple myeloma (MM), is a heterogeneous disease in which chromosomal abnormalities are important for prognostic risk stratification. Cytogenetic profiling with FISH on plasma cells from bone marrow samples (BM-PCs) is the current gold standard, but variable infiltration of plasma cells or failed aspiration can hamper this process. Ultra-low coverage sequencing (ULCS) of circulating cell-free DNA (ccfDNA) may offer a minimally invasive alternative for the work-up of these cases. We compared ULCS, aCGH and FISH on selected BM-PCs in a routine setting with ULCS of ccfDNA for the detection of somatic copy number aberrations (CNAs) in MM. METHODS: Purified CD138+ BM-PCs of 23 MM patients at initiation of their treatment were subjected to aCGH, FISH and ULCS. Paired samples of peripheral blood-ccfDNA obtained at diagnosis were analyzed by ULCS and compared to the results found in BM-PCs. RESULTS: Using ULCS of ccfDNA, cytogenetic markers were identified in 18 out of 23 patients; five cases could not be analyzed due to low (≤3%) tumor fraction (TF). High similarity between CNA profiles of BM-PCs and ccfDNA was found. Moreover, 78% of the ccfDNA profiles resulted in the same risk classification as the routine FISH and/or BM-PCs ULCS and aCGH. Chromothripsis was detected in five patients; these had the highest TF values (range 7.1% to 42%) in our series and their profiles showed other high-risk anomalies. CONCLUSION: This proof-of-principle study indicates that ULCS of ccfDNA can reveal CNAs in MM and should be explored further as a cost-efficient alternative, especially in cases where BM-PC purification fails.

Noninvasive prenatal testing detected acute myeloid leukemia in paucisymptomatic pregnant patient.

To the authors' best knowledge, this is the first report of acute myeloid leukemia (AML) detected by noninvasive prenatal testing. This was an aggressive case that otherwise would have been difficult to characterize due to disadvantages of "gold-standard" techniques.

Atypical chromosome 22q11.2 deletions are complex rearrangements and have different mechanistic origins.

The majority (99%) of individuals with 22q11.2 deletion syndrome (22q11.2DS) have a deletion that is caused by non-allelic homologous recombination between two of four low copy repeat clusters on chromosome 22q11.2 (LCR22s). However, in a small subset of patients, atypical deletions are observed with at least one deletion breakpoint within unique sequence between the LCR22s. The position of the chromosome breakpoints and the mechanisms driving those atypical deletions remain poorly studied. Our large-scale, whole genome sequencing study of >1500 subjects with 22q11.2DS identified six unrelated individuals with atypical deletions of different types. Using a combination of whole genome sequencing data and fiber-fluorescence in situ hybridization, we mapped the rearranged alleles in these subjects. In four of them, the distal breakpoints mapped within one of the LCR22s and we found that the deletions likely occurred by replication-based mechanisms. Interestingly, in two of them, an inversion probably preceded inter-chromosomal 'allelic' homologous recombination between differently oriented LCR22-D alleles. Inversion associated allelic homologous recombination (AHR) may well be a common mechanism driving (atypical) deletions on 22q11.2.

Male patient 46,XX SRY-negative and unambiguous genitalia: A case report / Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso / Male patient 46, XX SRY -negative and unambiguous genitalia: A case report

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

CARACTERIZACIÓN CITOGENÉTICA EN INDIVIDUOS DEL GÉNERO Lagothrix EN COLOMBIA (PRIMATES: ATELIDAE) / Cytogenetic Characterization in Individuals of the Genus Lagothrix in Colombia (Primates: Atelidae)

El género Lagothrix se encuentra representado en Colombia por Lagothrix lagothricha lagothricha y Lagothrix lagothricha lugens y siendo un género llamativo para el tráfico y caza, se han realizado varios trabajos encaminados a conocer sobre su ecología y ciclo de vida mostrando la importancia de este género en el ecosistema aunque sus características citogenéticas no han sido bien estudiadas. En este trabajo se analizaron 18 individuos (seis, L. l. lugens y 12 L. L. lagothricha) en cautiverio provenientes de zoológicos y centros de rescate, en los que por medio de técnicas de cultivo de sangre periférica y bandaje cromosómico G, C, R, Q y NOR se determinó un cariotipo estándar de 2n=62 para todos los individuos con dos variantes de éste también conocidos como cariomorfos que se originan por la diferencia en su número fundamental (NF), debido a una inversión pericéntrica en el par cromosómico 24. Dentro de estos cariomorfos se encontraron polimorfismos en varios pares cromosómicos que no fueron determinantes para diferenciar subespecies en los individuos trabajados, por lo que se recomienda revisar la taxonomía del género.

The genus Lagothrix is represented in Colombia by Lagothrix lagothricha lagothricha and Lagothrix lagothricha lugens but their cytogenetic features have not been well characterized. We studied 18 captive individuals (6, L. l. lugens and 12, L. L. lagothricha) from zoos and rescue centers, using techniques of peripheral blood culture and G, C, R, Q and NOR chromosome banding. We determined the standard karyotype 2n = 62 for all analyzed individuals with two karyotype variants (also known as karyomorphs) that showed different fundamental numbers due to a pericentric inversion on chromosome pair 24. Within these karyomorphs other polymorphisms were found in several pairs that were not crucial to distinguishing subspecies. We recommend reviewing the taxonomy of the genus especially at the subspecies level.

How many species of woolly monkeys inhabit Colombian forests?

There is a controversy regarding how many species the genus Lagothrix contains, since the Lagothrix lagothricha subspecies have been recently proposed to be actual species. Clarification of species status is of particular importance in the case of L. l. lugens, because it is the most endangered and its distribution is restricted to the Colombian Andes, a highly deforested region. Using cytogenetic and molecular markers, we obtained evidence indicating that the subspecies status is appropriate for the two taxa occurring in this country. We also report high levels of intraspecific variability in the karyotype. We find evidence for a late Pleistocene separation of the subspecies, and we propose it is the limited area of contact between the taxa that allowed for them to partially differentiate.