Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscape

Acknowledgements We dedicate this article to Maria Guida Boavida who founded the Human Genetics Laboratory as the precursor of the current Department of Human Genetics at the National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal. She and her colleagues performed the first chromosomal prenatal diagnosis from cultured amniocytes in Portugal in July 1977 (no. 77180). However, the first translocation in PND, a paternally inherited Robertsonian t(13;14) (no. 80321), was only identified in June 1980. Almost 40 years later, we report application of an liGS-based approach for the identification of dnBCAs breakpoints in PND. First, we are grateful to the family members for their involvement in this study. We thank Dr. Michael Talkowski and members of his lab for library preparation and sequencing data generation. We thank Jader Cruz for echographic diagnosis of fetal heart defects, to Hildeberto Correia, Ana Cristina Alves and Bárbara Marques for conventional prenatal diagnosis, and to Márcia Rodrigues, Sofia Nunes, Teresa Kay, and Rui Gonçalves for their contribution to the project.We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints. Identification of autosomal dominant disease due to the disruption of ANKS1B and WDR26 by t(12;17)(q23.1;q21.33)dn and t(1;3)(q24.11;p25.3)dn breakpoints, respectively, substantiated the proposed workflow. We then applied this workflow to two ongoing prenatal cases with apparently balanced dnBCAs: 46,XX,t(16;17)(q24;q21.3)dn referred for increased risk on combined first trimester screening and 46,XY,t(2;19)(p13;q13.1)dn referred due to a previous trisomy 21 pregnancy. Translocation breakpoints in the t(16;17) involve ANKRD11 and WNT3 and disruption of ANKRD11 resulted in KBG syndrome confirmed in postnatal follow-up. Breakpoints in the t(2;19) are within ATP6V1B1 and the 3' UTR of CEP89, and are not interpreted to cause disease. Genotype-phenotype correlation confirms the causative role of WDR26 in the Skraban-Deardorff and 1q41q42 microdeletion phenocopy syndromes, and that disruption of ANKS1B causes ANKS1B haploinsufficiency syndrome. In sum, we show that an liGS-based approach can be realized in PND care providing additional information concerning clinical outcomes of dnBCAs in patients with such rearrangements.C.C.M. is supported (GM061354) by the National Institutes of Health (USA) and the NIHR Manchester Biomedical Research Centre, UK. This research was supported by national funds through FCT—Fundação para a Ciência e a Tecnologia, Research Grant HMSP-ICT/0016/2013 of the Harvard Medical School—Portugal Program in Translational Research and Informationinfo:eu-repo/semantics/publishedVersio

Fracionamento densimétrico com politungstato de sódio no estudo da proteção física da matéria orgânica em solos Densimetric fractionation with sodium polytungstate to investigate physical protection of soil organic matter

O fracionamento físico densimétrico é uma técnica que permite estudar a proteção física da matéria orgânica (MO) no solo, sendo utilizadas, de forma indistinta, soluções densas de iodeto de sódio (NaI) e de politungstato de sódio (PTS). O objetivo deste estudo foi avaliar (a) o efeito de soluções de NaI (1,8 g cm-3) e de PTS (1,8, 2,0 e 2,2 g cm-3) no rendimento de carbono (C) nas frações leve-livre (FLL) e leve-oclusa (FLO) da MO na camada de 0-5 cm de um Argissolo Vermelho [PVd, Eldorado do Sul (RS)] e de um Latossolo Vermelho [LVdf, Dourados (MS)] e (b) a magnitude da proteção física da MO em agregados no acúmulo de C orgânico nesses solos submetidos, respectivamente, ao sistema plantio direto por 18 anos (PD) e pastagem (Brachiaria decumbens) por nove anos, em comparação à sua condição em preparo convencional (PC). Em ambos os locais, blocos indeformados de solo foram coletados em experimentos de longa duração; os agregados foram separados nos planos de fraqueza e passados em peneira de 9,51 mm; esse material foi submetido ao fracionamento densimétrico da MO do solo. O uso da solução de PTS 1,8 g cm-3 aumentou de 176 a 727 % o rendimento de C na FLO em comparação à solução de NaI na mesma densidade, mas não teve efeito no rendimento de C da FLL da MO do solo. O aumento da densidade da solução de PTS de 1,8 g cm-3 para 2,0 g cm-3 incrementou de 30 a 99 % o rendimento de C da FLO; contudo, o aumento da densidade para 2,2 g cm-3 resultou em aumento pouco expressivo (< 18 %) no rendimento de C na FLO nos diferentes solos e sistemas de manejo. O uso de NaI no fracionamento densimétrico leva à conclusão errônea de que a proteção física não é um mecanismo importante de estabilização da MO no solo. Por outro lado, a utilização da solução de PTS 2,0 g cm-3, a qual é recomendada para o fracionamento densimétrico devido à sua alta eficiência na recuperação do C da FLO, permitiu constatar que a proteção física da MO em agregados de solo foi responsável por 54 e 23 % do acúmulo de C orgânico no PVd e LVdf, respectivamente, sob plantio direto e pastagem.<br>Through the densimetric fractionation it is possible to study the physical protection of soil organic matter (SOM). High density solutions of sodium iodide (NaI) or sodium polytungstate (SPT) have been indistinctively used for this purpose. This study aimed to assess: (a) the capacity of these two solutions at a density of 1.8 g cm-3 (NaI-1.8 and SPT-1.8) and of SPT at densities of 2.0 (SPT-2.0) and 2.2 g cm-3 (SPT-2.2) to increase C recovery in the free light fraction (FLF) and occluded light fraction (OLF) of the organic matter contained in soil aggregates of the 0-5 cm layer of an Acrisol [PVd, Eldorado do Sul (RS)] and of a Ferralsol [LVdf, Dourados (MS)]; and (b) the magnitude of the physical protection in promoting soil organic matter accumulation in these soils under no-tillage for 18 years and pasture (Brachiaria decumbens) for 9 years, respectively, both in comparison to conventional-tilled soil. Soil blocks were collected and < 9.51 mm soil aggregates were separated and submitted to density fractionation of soil OM. The SPT-1.8 increased OLF-C by 176 to 726 % in comparison to NaI-1.8, but no effect was observed on FLF-C recovery. By using SPT-2.0, the OLF-C recovery increased by 30 to 90 % in comparison with SPT-1.8, but a lower increment (< 18 %) was observed when SPT-2.0 was substituted by SPT-2.2. Density fractionation of OM with NaI solution (low OLF and high FLF) may lead to the erroneous conclusion that physical protection is not an important stabilizing mechanism of SOM in soils under no-tillage or pasture. On the other hand, when using SPT-2.0, which was most efficient in recovering OLF-C, the physical protection within aggregates was responsible for 54 % (PVd) and 23 % (LVdf) of the total SOM accumulation in soils under no-tillage and pasture, respectively

Koolen-de Vries syndrome – National Case Series with clinical and molecular characterization

Introduction: Koolen-de Vries Syndrome (KdVS) is a rare genetic condition, caused by a 17q21.31 microdeletion, or a pathogenic variant in KANSL1 gene. The clinical picture includes developmental delay (DD)/intellectual disability (ID) with expressive language particularly impaired, dysmorphisms, neonatal hypotonia, and friendly behaviour. Aim: To characterize at the molecular and clinical levels all patients in Portugal diagnosed with KdVS.N/