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Caroselli S, Figliuzzi M, Picchetta L, Cogo F, Zambon P, Pergher I, Girardi L, Patassini C, Poli M, Bakalova D, Cimadomo D, Findikli N, Coban O, Serdarogullari M, Favero F, Bortolato S, Anastasi A, Capodanno F, Gallinelli A, Brancati F, Rienzi L, Ubaldi FM, Jimenez-Almazán J, Blesa-Jarque D, Miravet-Valenciano J, Rubio C, Simòn C, Capalbo A. Improved clinical utility of preimplantation genetic testing through the integration of ploidy and common pathogenic microdeletions analyses. Hum Reprod 2023; 38:762-775. [PMID: 36824049 DOI: 10.1093/humrep/dead033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/28/2023] [Indexed: 02/25/2023] Open
Abstract
STUDY QUESTION Can chromosomal abnormalities beyond copy-number aneuploidies (i.e. ploidy level and microdeletions (MDs)) be detected using a preimplantation genetic testing (PGT) platform? SUMMARY ANSWER The proposed integrated approach accurately assesses ploidy level and the most common pathogenic microdeletions causative of genomic disorders, expanding the clinical utility of PGT. WHAT IS KNOWN ALREADY Standard methodologies employed in preimplantation genetic testing for aneuploidy (PGT-A) identify chromosomal aneuploidies but cannot determine ploidy level nor the presence of recurrent pathogenic MDs responsible for genomic disorders. Transferring embryos carrying these abnormalities can result in miscarriage, molar pregnancy, and intellectual disabilities and developmental delay in offspring. The development of a testing strategy that integrates their assessment can resolve current limitations and add valuable information regarding the genetic constitution of embryos, which is not evaluated in PGT providing new level of clinical utility and valuable knowledge for further understanding of the genomic causes of implantation failure and early pregnancy loss. To the best of our knowledge, MDs have never been studied in preimplantation human embryos up to date. STUDY DESIGN, SIZE, DURATION This is a retrospective cohort analysis including blastocyst biopsies collected between February 2018 and November 2021 at multiple collaborating IVF clinics from prospective parents of European ancestry below the age of 45, using autologous gametes and undergoing ICSI for all oocytes. Ploidy level determination was validated using 164 embryonic samples of known ploidy status (147 diploids, 9 triploids, and 8 haploids). Detection of nine common MD syndromes (-4p=Wolf-Hirschhorn, -8q=Langer-Giedion, -1p=1p36 deletion, -22q=DiGeorge, -5p=Cri-du-Chat, -15q=Prader-Willi/Angelman, -11q=Jacobsen, -17p=Smith-Magenis) was developed and tested using 28 positive controls and 97 negative controls. Later, the methodology was blindly applied in the analysis of: (i) 100 two pronuclei (2PN)-derived blastocysts that were previously defined as uniformly euploid by standard PGT-A; (ii) 99 euploid embryos whose transfer resulted in pregnancy loss. PARTICIPANTS/MATERIALS, SETTING, METHODS The methodology is based on targeted next-generation sequencing of selected polymorphisms across the genome and enriched within critical regions of included MD syndromes. Sequencing data (i.e. allelic frequencies) were analyzed by a probabilistic model which estimated the likelihood of ploidy level and MD presence, accounting for both sequencing noise and population genetics patterns (i.e. linkage disequilibrium, LD, correlations) observed in 2504 whole-genome sequencing data from the 1000 Genome Project database. Analysis of phased parental haplotypes obtained by single-nucleotide polymorphism (SNP)-array genotyping was performed to confirm the presence of MD. MAIN RESULTS AND THE ROLE OF CHANCE In the analytical validation phase, this strategy showed extremely high accuracy both in ploidy classification (100%, CI: 98.1-100%) and in the identification of six out of eight MDs (99.2%, CI: 98.5-99.8%). To improve MD detection based on loss of heterozygosity (LOH), common haploblocks were analyzed based on haplotype frequency and LOH occurrence in a reference population, thus developing two further mathematical models. As a result, chr1p36 and chr4p16.3 regions were excluded from MD identification due to their poor reliability, whilst a clinical workflow which incorporated parental DNA information was developed to enhance the identification of MDs. During the clinical application phase, one case of triploidy was detected among 2PN-derived blastocysts (i) and one pathogenic MD (-22q11.21) was retrospectively identified among the biopsy specimens of transferred embryos that resulted in miscarriage (ii). For the latter case, family-based analysis revealed the same MD in different sibling embryos (n = 2/5) from non-carrier parents, suggesting the presence of germline mosaicism in the female partner. When embryos are selected for transfer based on their genetic constitution, this strategy can identify embryos with ploidy abnormalities and/or MDs beyond aneuploidies, with an estimated incidence of 1.5% (n = 3/202, 95% CI: 0.5-4.5%) among euploid embryos. LIMITATIONS, REASONS FOR CAUTION Epidemiological studies will be required to accurately assess the incidence of ploidy alterations and MDs in preimplantation embryos and particularly in euploid miscarriages. Despite the high accuracy of the assay developed, the use of parental DNA to support diagnostic calling can further increase the precision of the assay. WIDER IMPLICATIONS OF THE FINDINGS This novel assay significantly expands the clinical utility of PGT-A by integrating the most common pathogenic MDs (both de novo and inherited ones) responsible for genomic disorders, which are usually evaluated at a later stage through invasive prenatal testing. From a basic research standpoint, this approach will help to elucidate fundamental biological and clinical questions related to the genetics of implantation failure and pregnancy loss of otherwise euploid embryos. STUDY FUNDING/COMPETING INTEREST(S) No external funding was used for this study. S.C., M.F., F.C., P.Z., I.P., L.G., C.P., M.P., D.B., J.J.-A., D.B.-J., J.M.-V., and C.R. are employees of Igenomix and C.S. is the head of the scientific board of Igenomix. A.C. and L.P. are employees of JUNO GENETICS. Igenomix and JUNO GENETICS are companies providing reproductive genetic services. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- S Caroselli
- Reproductive Genetics, Igenomix Italia, Rome, Italy
| | - M Figliuzzi
- Reproductive Genetics, Igenomix Italia, Rome, Italy
| | | | - F Cogo
- Reproductive Genetics, Igenomix Italia, Marostica, Italy
| | - P Zambon
- Reproductive Genetics, Igenomix Italia, Marostica, Italy
| | - I Pergher
- Reproductive Genetics, Igenomix Italia, Marostica, Italy
| | - L Girardi
- Reproductive Genetics, Igenomix Italia, Marostica, Italy
| | - C Patassini
- Reproductive Genetics, Igenomix Italia, Marostica, Italy
| | - M Poli
- Reproductive Genetics, Igenomix Italia, Rome, Italy
| | - D Bakalova
- Reproductive Genetics, Igenomix UK, Guildford, UK
| | - D Cimadomo
- ART Center, Clinica Valle Giulia-GeneraLife IVF, Rome, Italy
| | - N Findikli
- Embryology Laboratory, Bahceci Fulya IVF Centre, Istanbul, Turkey
| | - O Coban
- Embryology Laboratory, British Cyprus IVF Hospital, Nicosia, Cyprus
| | - M Serdarogullari
- Department of Histology and Embryology, Faculty of Medicine Cyprus International University, Nicosia, North Cyprus
| | - F Favero
- ART Center, ARC-STER, Venice, Italy
| | | | - A Anastasi
- Physiopathology of Human Reproduction Center, Hospital "del Delta", Lagosanto, Italy
| | - F Capodanno
- Physiopathology of Human Reproduction Center, Hospital "del Delta", Lagosanto, Italy
| | - A Gallinelli
- Physiopathology of Human Reproduction Center, Hospital "del Delta", Lagosanto, Italy
| | - F Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy.,IRCCS San Raffaele Roma, Roma, Italy
| | - L Rienzi
- ART Center, Clinica Valle Giulia-GeneraLife IVF, Rome, Italy.,Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - F M Ubaldi
- ART Center, Clinica Valle Giulia-GeneraLife IVF, Rome, Italy
| | | | | | | | - C Rubio
- Reproductive Genetics, Igenomix Spain, Valencia, Spain
| | - C Simòn
- Reproductive Genetics, Igenomix Foundation, Valencia, Spain.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Harvard University, Harvard School of Medicine, Boston, MA, USA.,Department of Obstetrics and Gynecology, Valencia University and INCLIVA, Valencia, Spain
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Caroselli S, Figliuzzi M, Cogo F, Zambon P, Favero F, Anastasi A, Capodanno F, Gallinelli A, Cimadomo D, Rienzi L, Ubaldi F, Miravet-Valenciano J, Blesa-Jarque D, Simon C, Capalbo A. P-555 Improved clinical validity of Preimplantation Genetic Testing for Aneuploidy (PGT-A) using a next-generation sequencing workflow for simultaneous detection of aneuploidy, ploidy and common pathogenic microdeletions. Hum Reprod 2022. [DOI: 10.1093/humrep/deac107.513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Study question
Can chromosomal abnormalities beyond aneuploidies (i.e., ploidy and microdeletions, MD) be detected on a single trophectoderm (TE) embryo biopsy using a next-generation sequencing (NGS)-based workflow?
Summary answer
This NGS-based integrated approach allows accurate detection of ploidy status and the most common microdeletions from a single TE-biopsy,expanding PGT-A clinical validity and diagnostic capabilities.
What is known already
Standard methodologies employed in PGT-A do not determine embryo ploidy status due to the normalization process during copy-number-variation analysis. Transferring embryos with abnormal ploidy variations is expected to result in miscarriage or molar pregnancy. Common pathogenic MD are undetected as they fall below the PGT-A resolution limit (<10Mb). MD are involved in genomic disorders associated with neurodevelopmental disabilities and multiple congenital anomalies. The development of this sequencing strategy can resolve current limitations and add valuable information regarding the genetic constitution of embryos, which is not usually evaluated in PGT and normally requires the use of later-stage invasive prenatal diagnosis.
Study design, size, duration
Ploidy determination was validated using 244 embryo samples of known ploidy status (226 diploids, 10 triploids, 8 haploids). We analysed nine common MD syndromes (-4p=Wolf-Hirschhorn, -8q=Langer-Giedion, -1p=1p36 deletion, -22q=DiGeorge, -5p=Cri-du-Chat, -15q=Prader-Willi/Angelman, -11q=Jacobsen, -17p=Smith-Magenis) using 24 positive controls (amniocentesis DNA from MD cases or TE biopsies from autosomal monosomy mimicking MD) and 96 negative controls (healthy newborns). Overall, the dataset included 72 cases of individual chromosomal abnormalities and 576 negative cases across the eight MD regions.
Participants/materials, setting, methods
PGT-A products were reamplified and sequenced (IonTorrentS5-ThermoFisher) using a custom AmpliSeq panel targeting 384 regions with at least one Single Nucleotide Polymorphism (SNP) of high B-allelic frequency. A bioinformatic algorithm based on gaussian-mixture modelling of sequencing data was developed. This algorithm calculates the conditional probability of the observed B-allelic ratio for each SNP, depending on the copy number, then estimates the likelihood of ploidy and the presence of MD based on the sequencing outcomes.
Main results and the role of chance
Ploidy was correctly determined in 233/234 cases (Accuracy=99.4%), with only one diploid sample misclassified as triploid (PPV=94.1%, NPV=100%, Non-informative rate=9/243=3.1%).
Microdeletions could be consistently detected with high reliability in 6 out of the 8 considered regions (-8q,-22q,-5p,-15q,-11q and -17p; PPV=98.5%, NPV=99.5%). Detection of microdeletions of 1p and 4p were less reliable due to the presence of recurrent haplotype blocks in the population at those genomic regions, as confirmed by the analysis of a dataset of 2504 whole genome sequencing from One Thousand Genome Project database (1kGP). The only MD false positive case showed extended loss of heterozygosity in the microdeletion region (-22q), which might be related to uniparental disomy or consanguinity and requires further testing in the family.
This analytical framework was blindly applied to: (i) the analysis of 9 embryos from a family affected by DiGeorge syndrome (female partner was carrier of del22.q11.21(20754422-21440514), resulting in all embryos classified consistently with the conventional PGT-M results (using indirect linkage analysis); (ii) the analysis of samples from 99 transferred human euploid embryos resulting in pregnancy losses. No ploidy alteration was detected in miscarried euploid embryos, but 2 microdeletions (-8q, -22q) were found, with an estimated prevalence of 2/99 in the miscarriage population.
Limitations, reasons for caution
Larger cohort studies will be required to accurately assess the incidence of ploidy alterations and microdeletions in preimplantation embryos and particularly in euploid miscarriages. Despite the high accuracy of the assay developed, the use of parental DNA to support diagnostic calling can further increase the precision of the assay.
Wider implications of the findings
This study provides, for the first time, detection of common pathogenic microdeletions and ploidy status from a single TE biopsy, expanding PGT-A clinical validity. This new assay will also help elucidate fundamental biological and clinical questions related to the genetics of implantation failure and pregnancy loss of apparently euploid embryos.
Trial registration number
not applicable
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Affiliation(s)
- S Caroselli
- Igenomix Italia, Reproductive Genetics , Rome, Italy
| | - M Figliuzzi
- Igenomix Italia, Reproductive Genetics , Rome, Italy
| | - F Cogo
- Igenomix Italia, Reproductive Genetics , Marostica, Italy
| | - P Zambon
- Igenomix Italia, Reproductive Genetics , Marostica, Italy
| | - F Favero
- Arc-Ster, ART center , Mestre, Italy
| | - A Anastasi
- Hospital “del Delta”, Physiopathology of Human Reproduction Center , Lagosanto, Italy
| | - F Capodanno
- Hospital “del Delta”, Physiopathology of Human Reproduction Center , Lagosanto, Italy
| | - A Gallinelli
- Hospital “del Delta”, Physiopathology of Human Reproduction Center , Lagosanto, Italy
| | | | - L Rienzi
- GeneraLife, ART center , Rome, Italy
| | | | | | | | - C Simon
- Igenomix Spain, Reproductive Genetics , Valencia, Spain
| | - A Capalbo
- Igenomix Italia, Reproductive Genetics , Rome, Italy
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Capalbo A, Fabiani M, Caroselli S, Poli M, Girardi L, Patassini C, Favero F, Cimadomo D, Vaiarelli A, Simon C, Rienzi LF, Ubaldi FM. Clinical validity and utility of preconception expanded carrier screening for the management of reproductive genetic risk in IVF and general population. Hum Reprod 2021; 36:2050-2061. [PMID: 34021342 DOI: 10.1093/humrep/deab087] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/15/2021] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION What is the clinical validity and utility of preconception Expanded Carrier Screening (ECS) application on the management of prospective parents? SUMMARY ANSWER The high detection rate of at-risk couples (ARCs) and the high proportion opting for IVF/preimplantation genetic testing (PGT) treatment demonstrate the clinical utility of ECS in the preconception space in IVF and general population. WHAT IS KNOWN ALREADY About 2-4% of couples are at risk of conceiving a child with an autosomal recessive or X-linked genetic disorder. In recent years, the increasing cost-effectiveness of genetic diagnostic techniques has allowed the creation of ECS panels for the simultaneous detection of multiple recessive disorders. Comprehensive preconception genetic screening holds the potential to significantly improve couple's genetic risk assessment and reproductive planning to avoid detectable inheritable genetic offspring. STUDY DESIGN, SIZE, DURATION A total of 3877 individuals without a family history of genetic conditions were analyzed between January 2017 and January 2020. Of the enrolled individuals, 1212 were gamete donors and 2665 were patients planning on conceiving from both the IVF and the natural conception group. From the non-donor cohort, 1133 were analyzed as individual patients, while the remaining ones were analyzed as couples, for a total of 766 couples. PARTICIPANTS/MATERIALS, SETTING, METHODS A focused ECS panel was developed following American College of Obstetrics and Gynecology ACOG-recommended criteria (prevalence, carrier rate, severity), including highly penetrant severe childhood conditions. Couples were defined at-risk when both partners carried an autosomal recessive pathogenic/likely pathogenic variant (PLP) on the same gene or when the woman was a carrier of an X-linked PLP variant. ARC detection rate defined the clinical validity of the ECS approach. Clinical utility was evaluated by monitoring ARCs reproductive decision making. MAIN RESULTS AND THE ROLE OF CHANCE A total of 402 individuals (10.4%) showed PLP for at least one of the genes tested. Among the 766 couples tested, 173 showed one carrier partner (22.6%), whereas 20 couples (2.6%) were found to be at increased risk. Interestingly, one ARC was identified as a result of cascade testing in the extended family of an individual carrying a pathogenic variant on the Survival Of Motor Neuron 1SMN1 gene. Of the identified ARCs, 5 (0.7%) were at risk for cystic fibrosis, 5 (0.7%) for fragile X syndrome, 4 (0.5%) for spinal muscular atrophy, 4 (0.5%) for Beta-Thalassemia/Sickle Cell Anemia, 1 (0.1%) for Smith-Lemli-Opitz Syndrome and 1 (0.1%) for Duchenne/Becker Dystrophy. Fifteen ARCs were successfully followed up from both the IVF and the natural conception groups. All of these (15/15) modified their reproductive planning by undergoing ART with Preimplantation Genetic Testing for Monogenic disease and Aneuploidies (PGT-M and PGT-A). To date, 6/15 (40%) couples completed their PGT cycle with euploid/unaffected embryos achieving a pregnancy after embryo transfer and three of them have already had an unaffected baby. LIMITATIONS, REASONS FOR CAUTION The use of a limited panel of core gene-disease pairs represents a limitation on the research perspective as it can underestimate the rate of detectable carriers and ARCs in this cohort of prospective parents. Expanding the scope of ECS to a larger panel of conditions is becoming increasingly feasible, thanks to a persistent technological evolution and progressive cataloging of gene-disease associations. WIDER IMPLICATIONS OF THE FINDINGS These results highlight the potential clinical validity and utility of ECS in reducing the risk of a pregnancy affected by a detectable inheritable genetic condition. The steady reduction in the costs of genetic analyses enables the expansion of monogenic testing/screening applications at the preimplantation stage, thus, providing valid decisional support and reproductive autonomy to patients, particularly in the context of IVF. STUDY FUNDING/COMPETING INTEREST(S) No external funding was used for this study. A.C., M.F., S.C., M.P., L.G., and C.P. are employees of Igenomix Italy. C.S. is the head of the scientific board of Igenomix. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- A Capalbo
- Igenomix Italy, Marostica, Italy.,Igenomix Foundation, INCLIVA, Valencia, Spain
| | | | | | - M Poli
- Igenomix Italy, Marostica, Italy
| | | | | | | | - D Cimadomo
- GeneraLife, Center for Reproductive Medicine, Clinica Valle Giulia, Rome, Italy
| | - A Vaiarelli
- GeneraLife, Center for Reproductive Medicine, Clinica Valle Giulia, Rome, Italy
| | - C Simon
- Igenomix Italy, Marostica, Italy.,Igenomix Foundation, INCLIVA, Valencia, Spain.,Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain.,Department of Obstetrics and Gynecology BIDMC, Harvard University, Cambridge, MA, USA
| | - L F Rienzi
- GeneraLife, Center for Reproductive Medicine, Clinica Valle Giulia, Rome, Italy
| | - F M Ubaldi
- GeneraLife, Center for Reproductive Medicine, Clinica Valle Giulia, Rome, Italy
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Jørgensen GØ, Favero F, Schmidt Jespersen J, Tulstrup MR, Rodriguez‐Gonzalez FG, Nielsen AF, Sørensen B, Ebbesen LH, Bæch J, Haastrup EK, Nielsen C, Josefsson PL, Thorsgaard M, El‐Galaly TC, Brown P, Weischenfeldt JL, Larsen TS, Grønbæk K, Husby S. CLINICAL IMPACT OF T‐CELL RECEPTOR REPERTOIRE DIVERSITY IN PATIENTS WITH LYMPHOMA UNDERGOING AUTOLOGOUS STEM CELL TRANSPLANTATION. Hematol Oncol 2021. [DOI: 10.1002/hon.1_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - F Favero
- Finsen laboratory Hematology‐Oncology, Rigshospitalet Copenhagen Denmark
| | | | | | | | - A. F Nielsen
- Rigshospitalet Dept. of Clinical Immunology Copenhagen Denmark
| | - B Sørensen
- Aarhus University Hospitalet Clinical Immunology Aarhus Denmark
| | - L. H Ebbesen
- Aarhus University Hospital Clinical Immunology Aarhus Denmark
| | - J Bæch
- Aalborg University Hospital Clinical Immunology Aalborg Denmark
| | - E. K Haastrup
- Rigshospitalet Dept. of Clinical Immunology Copenhagen Denmark
| | - C Nielsen
- Odense University Hospital Dept. of Clinical Immunology Copenhagen Denmark
| | | | - M Thorsgaard
- Aarhus University Hospital Hematology Aarhus Denmark
| | | | - P Brown
- Rigshospitalet Hematology Copenhagen N Denmark
| | - J. L Weischenfeldt
- Finsen laboratory Hematology‐Oncology, Rigshospitalet Copenhagen Denmark
| | - T. S Larsen
- Odense University Hospital Hematology Odense Denmark
| | - K Grønbæk
- Rigshospitalet Hematology Copenhagen N Denmark
| | - S Husby
- Rigshospitalet Hematology Copenhagen N Denmark
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Calizza E, Favero F, Rossi D, Careddu G, Fiorentino F, Sporta Caputi S, Rossi L, Costantini ML. Isotopic biomonitoring of N pollution in rivers embedded in complex human landscapes. Sci Total Environ 2020; 706:136081. [PMID: 31862596 DOI: 10.1016/j.scitotenv.2019.136081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
The dynamic and hierarchical structure of rivers, together with disruption of the natural river continuum by human activities, makes it difficult to identify and locate sources of nutrient pollution affecting receiving waters and observe its dispersion, thus impairing monitoring efforts. The identification of reliable indicators of anthropogenic nitrogen inputs in catchments is therefore key to achieving effective management of polluted rivers. We tested the capacity of N isotopic signatures (δ15N) of epilithon and snails to provide useful indications of organic and inorganic anthropogenic N inputs in three Mediterranean rivers differing in terms of surrounding land use and physicochemical conditions. We used a combined approach based on (i) analysis of nutrient concentrations in water, (ii) CORINE land cover classification and drainage patterns in catchments and (iii) isotopic analysis of river biota to verify whether isotopic variations were indicative of anthropic activities in the watershed, the associated alteration of water quality, and the consequent impact on snail abundance and diversity. Variation in the δ15N of epilithon within and between rivers reflected localised and diffuse N inputs from inorganic and organic sources. Negative epilithon δ15N values (<0‰) indicated inorganic pollution from agriculture. Values between 4‰ and 8‰ and those above 8‰ respectively indicated moderate organic pollution from urban areas, and high organic pollution, mostly from waste waters. The diversity and abundance of snails decreased with increasing water pollution. While their isotopic variations reflected between-river differences, they failed to indicate within-river variations in anthropogenic N inputs, since the proportion of epilithon in their diet varied along the rivers. Concluding, epilithon was a reliable indicator of anthropogenic N sources across a wide range of nutrient concentrations and anthropogenic inputs, and the proposed approach allowed us to determine the nature of nitrogen pollutants, their sources, location and dispersion along rivers embedded in complex human landscapes.
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Affiliation(s)
- E Calizza
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy; CoNISMa, piazzale Flaminio 9, 00196 Rome, Italy
| | - F Favero
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy
| | - D Rossi
- CNR-Water Research Institute, Research Area RM1, via Salaria km 29.300 C.P.10, 00015 Monterotondo, RM, Italy
| | - G Careddu
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy
| | - F Fiorentino
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy
| | - S Sporta Caputi
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy.
| | - L Rossi
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy; CoNISMa, piazzale Flaminio 9, 00196 Rome, Italy
| | - M L Costantini
- Department of Environmental Biology, Sapienza University of Rome, via dei Sardi 70, 00185 Rome, Italy; CoNISMa, piazzale Flaminio 9, 00196 Rome, Italy
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Husby S, Favero F, Nielsen C, Sørensen B, Baech J, Hansen J, Rodriguez-Gonzalez F, Arboe B, Andersen P, Haastrup E, Fischer-Nielsen A, Saekmose S, Hansen P, Christiansen I, Clasen-Linde E, Knudsen L, Grell K, Segel E, Ebbesen L, Thorsgaard M, Josefsson P, El-Galaly T, Brown P, Weischenfeldt J, Larsen T, Grønbaek K. HIGH RISK OF ADVERSE EVENTS AFTER AUTOLOGOUS STEM-CELL TRANSPLANTATION IN LYMPHOMA PATIENTS WITH DNA REPAIR PATHWAY MUTATIONS: A NATION-WIDE COHORT STUDY. Hematol Oncol 2019. [DOI: 10.1002/hon.5_2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- S. Husby
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - F. Favero
- Biotech Research & Innovation Center (BRIC); University of Copenhagen; Copenhagen Denmark
| | - C. Nielsen
- Dept. of Immunology; Odense University Hospital; Odense Denmark
| | - B. Sørensen
- Dept. of Immunology; Aarhus University Hospital; Aarhus Denmark
| | - J. Baech
- Dept. of Immunology; Aalborg University Hospital; Aalborg Denmark
| | - J.W. Hansen
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | | | - B. Arboe
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - P.L. Andersen
- Dept. of Immunology; Herlev University Hospital; Herlev Denmark
| | - E.K. Haastrup
- Dept. of Immunology; Rigshospitalet; Copenhagen Denmark
| | | | - S.G. Saekmose
- Dept. of Immunology; Roskilde University Hospital; Naestved Denmark
| | - P.B. Hansen
- Dept. of Hematology; Roskilde University Hospital; Roskilde Denmark
| | - I. Christiansen
- Dept. of Hematology; Aalborg University Hospitale; Aalborg Denmark
| | | | - L.M. Knudsen
- Dept. of Hematology; Herlev University Hospital; Herlev Denmark
| | - K. Grell
- Dept. of Biostatistics; University of Copenhagen; Copenhagen Denmark
| | - E.K. Segel
- Dept. of Hematology; Aarhus University Hospital; Aarhus Denmark
| | - L.H. Ebbesen
- Dept. of Hematology; Aarhus University Hospital; Aarhus Denmark
| | - M. Thorsgaard
- Dept. of Hematology; Aarhus University Hospital; Aarhus Denmark
| | - P.L. Josefsson
- Dept. of Hematology; Herlev University Hospital; Herlev Denmark
| | - T.C. El-Galaly
- Dept. of Hematology; Aalborg University Hospitale; Aalborg Denmark
| | - P.D. Brown
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - J. Weischenfeldt
- Biotech Research & Innovation Center (BRIC); University of Copenhagen; Copenhagen Denmark
| | - T.S. Larsen
- Dept. of Hematology; Odense University Hospital; Odense Denmark
| | - K. Grønbaek
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
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Husby S, Eskelund C, Favero F, Rodriguez-Gonzalez F, Kolstad A, Pedersen L, Räty R, Geisler C, Jerkeman M, Weischenfeldt J, Grønbaek K. EVOLUTION OF CLONAL HEMATOPOIESIS IN MANTLE CELL LYMPHOMA PATIENTS BEFORE, DURING, AND AFTER INDUCTION CHEMOTHERAPY AND AUTOLOGOUS STEM CELL TRANSPLANTATION. Hematol Oncol 2019. [DOI: 10.1002/hon.50_2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S. Husby
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - C.W. Eskelund
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - F. Favero
- Biotech Research & Innovation Center (BRIC); University of Copenhagen; Copenhagen N Denmark
| | | | - A. Kolstad
- Dept. of Oncology; Oslo University Hospital; Oslo Norway
| | - L.B. Pedersen
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - R. Räty
- Dept. of Hematology; Helsinki University Hospital; Helsinki Finland
| | - C.H. Geisler
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
| | - M. Jerkeman
- Dept. of Oncology; Lund University Hospital; Lund Sweden
| | - J. Weischenfeldt
- Biotech Research & Innovation Center (BRIC); University of Copenhagen; Copenhagen N Denmark
| | - K. Grønbaek
- Dept. of Hematology; Rigshospitalet; Copenhagen N Denmark
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Artilheiro M, Oliveira E, Carvas N, Favero F, Caromano F, Sá C, Voos M. DUCHENNE MUSCULAR DYSTROPHY - PHYSIOTHERAPY. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Giuffrida R, Conforti C, Resende FSS, Hamilko de Barros M, Uranitsch M, Favero F, Deinlein T, Hofmann-Wellenhof R, Zalaudek I. Clinical and dermoscopic features of genital pigmented Bowen disease. Clin Exp Dermatol 2018; 43:813-816. [DOI: 10.1111/ced.13633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
- R. Giuffrida
- Department of Clinical and Experimental Medicine; Section of Dermatology; University of Messina; Messina Italy
| | - C. Conforti
- Department of Dermatology and Venereology; University of Graz; Graz Austria
| | - F. S. S. Resende
- Department of Dermatology and Venereology; University of Graz; Graz Austria
| | - M. Hamilko de Barros
- Professor Rubem David Azulay Institute; Charity Hospital of Rio de Janeiro; Rio de Janeiro Brazil
| | - M. Uranitsch
- Department of Dermatology and Venereology; University of Graz; Graz Austria
| | - F. Favero
- Department of Dermatology and Venereology; University of Graz; Graz Austria
| | - T. Deinlein
- Department of Dermatology and Venereology; Medical University of Graz; Graz Austria
| | - R. Hofmann-Wellenhof
- Department of Dermatology and Venereology; Medical University of Graz; Graz Austria
| | - I. Zalaudek
- Department of Dermatology and Venereology; University of Trieste; Ospedale Maggiore Trieste Italy
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Voos M, Martini J, Simões M, Hukuda M, Favero F, Oliveira A, Caromano F. The relevance of timed movements on functional assessment in Duchenne muscular dystrophy. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Voos M, Marim J, Anequini I, Favero F, Carmo A, Oliveira A, Caromano F. Description of muscle strength in a Brazilian sample of limb-girdle muscular dystrophy 2A (calpainopathy). Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Voos M, Favero F, Dias K, Artiheiro M, Oliveira A, Caromano F. Dissociation between motor and cognitive skills in patients with Duchenne muscular dystrophy. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Favero F, McGranahan N, Salm M, Birkbak NJ, Sanborn JZ, Benz SC, Becq J, Peden JF, Kingsbury Z, Grocok RJ, Humphray S, Bentley D, Spencer-Dene B, Gutteridge A, Brada M, Roger S, Dietrich PY, Forshew T, Gerlinger M, Rowan A, Stamp G, Eklund AC, Szallasi Z, Swanton C. Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome. Ann Oncol 2015; 26:880-887. [PMID: 25732040 PMCID: PMC4405282 DOI: 10.1093/annonc/mdv127] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common malignant brain cancer occurring in adults, and is associated with dismal outcome and few therapeutic options. GBM has been shown to predominantly disrupt three core pathways through somatic aberrations, rendering it ideal for precision medicine approaches. METHODS We describe a 35-year-old female patient with recurrent GBM following surgical removal of the primary tumour, adjuvant treatment with temozolomide and a 3-year disease-free period. Rapid whole-genome sequencing (WGS) of three separate tumour regions at recurrence was carried out and interpreted relative to WGS of two regions of the primary tumour. RESULTS We found extensive mutational and copy-number heterogeneity within the primary tumour. We identified a TP53 mutation and two focal amplifications involving PDGFRA, KIT and CDK4, on chromosomes 4 and 12. A clonal IDH1 R132H mutation in the primary, a known GBM driver event, was detectable at only very low frequency in the recurrent tumour. After sub-clonal diversification, evidence was found for a whole-genome doubling event and a translocation between the amplified regions of PDGFRA, KIT and CDK4, encoded within a double-minute chromosome also incorporating miR26a-2. The WGS analysis uncovered progressive evolution of the double-minute chromosome converging on the KIT/PDGFRA/PI3K/mTOR axis, superseding the IDH1 mutation in dominance in a mutually exclusive manner at recurrence, consequently the patient was treated with imatinib. Despite rapid sequencing and cancer genome-guided therapy against amplified oncogenes, the disease progressed, and the patient died shortly after. CONCLUSION This case sheds light on the dynamic evolution of a GBM tumour, defining the origins of the lethal sub-clone, the macro-evolutionary genomic events dominating the disease at recurrence and the loss of a clonal driver. Even in the era of rapid WGS analysis, cases such as this illustrate the significant hurdles for precision medicine success.
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Affiliation(s)
- F Favero
- Cancer Research UK London Research Institute, London, United Kingdom; Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - N McGranahan
- Cancer Research UK London Research Institute, London, United Kingdom; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London
| | - M Salm
- Cancer Research UK London Research Institute, London, United Kingdom
| | - N J Birkbak
- Cancer Research UK London Research Institute, London, United Kingdom; University College London Cancer Institute, London, United Kingdom
| | | | | | | | | | | | | | | | | | - B Spencer-Dene
- Cancer Research UK London Research Institute, London, United Kingdom
| | - A Gutteridge
- University College London Cancer Institute, London, United Kingdom
| | - M Brada
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool; Department of Radiation Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, United Kingdom
| | - S Roger
- Department of Oncology, University Hospital Zurich, Zürich
| | - P-Y Dietrich
- Centre of Oncology, University Hospitals of Geneva, Geneva, Switzerland
| | - T Forshew
- University College London Cancer Institute, London, United Kingdom
| | - M Gerlinger
- Cancer Research UK London Research Institute, London, United Kingdom; Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - A Rowan
- Cancer Research UK London Research Institute, London, United Kingdom
| | - G Stamp
- Cancer Research UK London Research Institute, London, United Kingdom
| | - A C Eklund
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Z Szallasi
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, USA; MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, 2nd Department of Pathology, Semmelweis University, Budapest,Hungary
| | - C Swanton
- Cancer Research UK London Research Institute, London, United Kingdom; University College London Cancer Institute, London, United Kingdom.
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Abstract
BACKGROUND In many western countries individuals will need to continue their professional careers beyond the current retirement age. This requires adaptation of the working conditions to compensate for age related visual changes. OBJECTIVE The aim of this paper is to compile and structure knowledge concerning age related changes in visual and non-visual functions among older-age workers and to describe in what way these changes relate to light and work performance. METHOD An overview of the literature was performed in PubMed and EMBASE concerning visual changes among elderly people, light, visual ergonomics and consequences at work. RESULTS Visual conditions and lighting design have an impact on work performance in those over age 65 even if there are few studies available. Natural age related changes in the eyes or ocular diseases can result in reduced visual function and performance. Moreover, evidence of the importance of light and dark rhythms for circadian regulation is mounting; there are indications that the older-age population might need specific attention related to this issue. Finally, visual deteriorations might also, secondarily, induce strained postures and musculoskeletal symptoms, pain and injury. CONCLUSION Age-related changes in the eyes and also ocular diseases among older-age people have an impact on well-being and work performance, and therefore call for reconsideration of their working conditions. Knowledge about how visual functions, light and ocular diseases is needed for work design and preventive actions.
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Affiliation(s)
- P Nylén
- Division of Ergonomics, School of Technology and Health, KTH Royal Institute of Technology, Huddinge, Sweden Swedish Work Environment Authority, Stockholm, Sweden
| | - F Favero
- Lighting Laboratory, Division of Ergonomics, School of Technology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - S Glimne
- Division of Clinical Neuroscience, Karolinska Institutet, St. Erik Eye Hospital, Stockholm, Sweden
| | - K Teär Fahnehjelm
- Division of Clinical Neuroscience, Karolinska Institutet, St. Erik Eye Hospital, Stockholm, Sweden St. Erik Eye Hospital, Stockholm, Sweden
| | - J Eklund
- Division of Ergonomics, School of Technology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
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Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol 2015; 26:64-70. [PMID: 25319062 PMCID: PMC4269342 DOI: 10.1093/annonc/mdu479] [Citation(s) in RCA: 477] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Exome or whole-genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus, single nucleotide polymorphism (SNP) arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele-specific, copy number profiles from tumor sequencing data have been described. MATERIALS AND METHODS We developed Sequenza, a software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. We applied Sequenza, as well as two previously published algorithms, to exome sequence data from 30 tumors from The Cancer Genome Atlas. We assessed the performance of these algorithms by comparing their results with those generated using matched SNP arrays and processed by the allele-specific copy number analysis of tumors (ASCAT) algorithm. RESULTS Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson's r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30%. CONCLUSIONS The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale mutations but also for estimating cellularity and inferring DNA copy number aberrations.
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Affiliation(s)
- F Favero
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - T Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - A M Marquard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - N J Birkbak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - M Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Q Li
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Medical School, Xiamen University, Xiamen, China
| | - Z Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, USA
| | - A C Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
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