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Article: Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy.

Zerella, Jiarna R / Homan, Claire C / Arts, Peer / Brown, Anna L / Scott, Hamish S / Hahn, Christopher N

2023 Volume 13, Page(s) 1183318

Abstract: Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as ... ...

Abstract	Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
Language	English
Publishing date	2023-06-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1183318
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Article ; Online: Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications.

Sullivan, Patricia J / Gayevskiy, Velimir / Davis, Ryan L / Wong, Marie / Mayoh, Chelsea / Mallawaarachchi, Amali / Hort, Yvonne / McCabe, Mark J / Beecroft, Sarah / Jackson, Matilda R / Arts, Peer / Dubowsky, Andrew / Laing, Nigel / Dinger, Marcel E / Scott, Hamish S / Oates, Emily / Pinese, Mark / Cowley, Mark J

Genome biology

2023 Volume 24, Issue 1, Page(s) 118

Abstract: Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each ... ...

Abstract	Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each splicing context remains difficult. Here, we describe Introme, which uses machine learning to integrate predictions from several splice detection tools, additional splicing rules, and gene architecture features to comprehensively evaluate the likelihood of a variant impacting splicing. Through extensive benchmarking across 21,000 splice-altering variants, Introme outperformed all tools (auPRC: 0.98) for the detection of clinically significant splice variants. Introme is available at https://github.com/CCICB/introme .
MeSH term(s)	Humans ; RNA Splice Sites ; Introns ; RNA Splicing ; Machine Learning ; Mutation
Chemical Substances	RNA Splice Sites
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-02936-7
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Article ; Online: Variable expressivity in a four-generation ACDMPV family with a non-coding hypermorphic SNV in trans to the frameshifting FOXF1 variant.

Yıldız Bölükbaşı, Esra / Karolak, Justyna A / Szafranski, Przemyslaw / Gambin, Tomasz / Matsika, Admire / McManus, Sam / Scott, Hamish S / Arts, Peer / Ha, Thuong / Barnett, Christopher P / Rodgers, Jonathan / Stankiewicz, Paweł

European journal of human genetics : EJHG

2022 Volume 30, Issue 10, Page(s) 1182–1186

Abstract: Heterozygous single nucleotide variants (SNVs) or copy-number variant deletions involving FOXF1 or its distant lung-specific enhancer on chromosome 16q24.1 have been identified in 80-90% of patients with Alveolar capillary dysplasia with misalignment of ... ...

Abstract	Heterozygous single nucleotide variants (SNVs) or copy-number variant deletions involving FOXF1 or its distant lung-specific enhancer on chromosome 16q24.1 have been identified in 80-90% of patients with Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe a four-generation family with a deceased ACDMPV neonate, her sibling from the electively terminated pregnancy, healthy mother with a history of pulmonary arterial hypertension (PAH), an unaffected aunt, an aunt deceased due to findings consistent with ACDMPV, and a reportedly unaffected grandmother, all with the frameshifting variant c.881_902dup (p.Gly302Profs*46) in FOXF1, and a deceased great-grandmother with a history of PAH. Genome sequencing analyses in the proband's unaffected mother revealed a non-coding putative regulatory SNV rs560517434-A within the lung-specific distant FOXF1 enhancer in trans to the FOXF1 frameshift mutation. Functional testing of this variant using an in vitro luciferase reporter assay showed that it increased FOXF1 promoter activity 10-fold. Our studies further demonstrate that non-coding SNVs in the FOXF1 enhancer region can rescue the lethal ACDMPV phenotype and support the compound inheritance gene dosage model.
MeSH term(s)	Female ; Forkhead Transcription Factors/genetics ; Frameshift Mutation ; Humans ; Infant, Newborn ; Nucleotides ; Persistent Fetal Circulation Syndrome/genetics ; Pulmonary Alveoli/abnormalities ; Sequence Deletion
Chemical Substances	FOXF1 protein, human ; Forkhead Transcription Factors ; Nucleotides
Language	English
Publishing date	2022-07-28
Publishing country	England
Document type	Case Reports ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-022-01159-x
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Article ; Online: GATA2 deficiency syndrome: A decade of discovery.

Homan, Claire C / Venugopal, Parvathy / Arts, Peer / Shahrin, Nur H / Feurstein, Simone / Rawlings, Lesley / Lawrence, David M / Andrews, James / King-Smith, Sarah L / Harvey, Natasha L / Brown, Anna L / Scott, Hamish S / Hahn, Christopher N

Human mutation

2021 Volume 42, Issue 11, Page(s) 1399–1421

Abstract: GATA2 deficiency syndrome (G2DS) is a rare autosomal dominant genetic disease predisposing to a range of symptoms, of which myeloid malignancy and immunodeficiency including recurrent infections are most common. In the last decade since it was first ... ...

Abstract	GATA2 deficiency syndrome (G2DS) is a rare autosomal dominant genetic disease predisposing to a range of symptoms, of which myeloid malignancy and immunodeficiency including recurrent infections are most common. In the last decade since it was first reported, there have been over 480 individuals identified carrying a pathogenic or likely pathogenic germline GATA2 variant with symptoms of G2DS, with 240 of these confirmed to be familial and 24 de novo. For those that develop myeloid malignancy (75% of all carriers with G2DS disease symptoms), the median age of onset is 17 years (range 0-78 years) and myelodysplastic syndrome is the first diagnosis in 75% of these cases with acute myeloid leukemia in a further 9%. All variant types appear to predispose to myeloid malignancy and immunodeficiency. Apart from lymphedema in which haploinsufficiency seems necessary, the mutational requirements of the other less common G2DS phenotypes is still unclear. These predominantly loss-of-function variants impact GATA2 expression and function in numerous ways including perturbations to DNA binding, protein structure, protein:protein interactions, and gene transcription, splicing, and expression. In this review, we provide the first expert-curated ACMG/AMP classification with codes of published variants compatible for use in clinical or diagnostic settings.
MeSH term(s)	Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Cohort Studies ; GATA2 Deficiency/genetics ; GATA2 Transcription Factor/genetics ; Humans ; Infant ; Infant, Newborn ; Middle Aged ; Young Adult
Chemical Substances	GATA2 Transcription Factor ; GATA2 protein, human
Language	English
Publishing date	2021-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.24271
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Article ; Online: Compound heterozygous variants in LAMC3 in association with posterior periventricular nodular heterotopia.

De Angelis, Carla / Byrne, Alicia B / Morrow, Rebecca / Feng, Jinghua / Ha, Thuong / Wang, Paul / Schreiber, Andreas W / Babic, Milena / Taranath, Ajay / Manton, Nick / King-Smith, Sarah L / Schwarz, Quenten / Arts, Peer / Scott, Hamish S / Barnett, Christopher

BMC medical genomics

2021 Volume 14, Issue 1, Page(s) 64

Abstract: Background: Periventricular nodular heterotopia (PNH) is a malformation of cortical development characterized by nodules of abnormally migrated neurons. The cause of posteriorly placed PNH is not well characterised and we present a case that provides ... ...

Abstract	Background: Periventricular nodular heterotopia (PNH) is a malformation of cortical development characterized by nodules of abnormally migrated neurons. The cause of posteriorly placed PNH is not well characterised and we present a case that provides insights into the cause of posterior PNH. Case presentation: We report a fetus with extensive posterior PNH in association with biallelic variants in LAMC3. LAMC3 mutations have previously been shown to cause polymicrogyria and pachygyria in the occipital cortex, but not PNH. The occipital location of PNH in our case and the proposed function of LAMC3 in cortical development suggest that the identified LAMC3 variants may be causal of PNH in this fetus. Conclusion: We hypothesise that this finding extends the cortical phenotype associated with LAMC3 and provides valuable insight into genetic cause of posterior PNH.
MeSH term(s)	Brain ; Magnetic Resonance Imaging ; Periventricular Nodular Heterotopia
Language	English
Publishing date	2021-02-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1755-8794
ISSN (online)	1755-8794
DOI	10.1186/s12920-021-00911-4
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Article ; Online: Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses.

van Deuren, Rosanne C / Arts, Peer / Cavalli, Giulio / Jaeger, Martin / Steehouwer, Marloes / van de Vorst, Maartje / Gilissen, Christian / Joosten, Leo A B / Dinarello, Charles A / Mhlanga, Musa M / Kumar, Vinod / Netea, Mihai G / van de Veerdonk, Frank L / Hoischen, Alexander

Genome medicine

2021 Volume 13, Issue 1, Page(s) 94

Abstract: Background: The interleukin (IL)-1 pathway is primarily associated with innate immunological defense and plays a major role in the induction and regulation of inflammation. Both common and rare genetic variation in this pathway underlies various ... ...

Abstract	Background: The interleukin (IL)-1 pathway is primarily associated with innate immunological defense and plays a major role in the induction and regulation of inflammation. Both common and rare genetic variation in this pathway underlies various inflammation-mediated diseases, but the role of rare variants relative to common variants in immune response variability in healthy individuals remains unclear. Methods: We performed molecular inversion probe sequencing on 48 IL-1 pathway-related genes in 463 healthy individuals from the Human Functional Genomics Project. We functionally grouped common and rare variants, over gene, subpathway, and inflammatory levels and performed the Sequence Kernel Association Test to test for association with in vitro stimulation-induced cytokine responses; specifically, IL-1β and IL-6 cytokine measurements upon stimulations that represent an array of microbial infections: lipopolysaccharide (LPS), phytohaemagglutinin (PHA), Candida albicans (C. albicans), and Staphylococcus aureus (S. aureus). Results: We identified a burden of NCF4 rare variants with PHA-induced IL-6 cytokine and showed that the respective carriers are in the 1% lowest IL-6 producers. Collapsing rare variants in IL-1 subpathway genes produces a bidirectional association with LPS-induced IL-1β cytokine levels, which is reflected by a significant Spearman correlation. On the inflammatory level, we identified a burden of rare variants in genes encoding for proteins with an anti-inflammatory function with S. aureus-induced IL-6 cytokine. In contrast to these rare variant findings which were based on different types of stimuli, common variant associations were exclusively identified with C. albicans-induced cytokine over various levels of grouping, from the gene, to subpathway, to inflammatory level. Conclusions: In conclusion, this study shows that functionally grouping common and rare genetic variants enables the elucidation IL-1-mediated biological mechanisms, specifically, for IL-1β and IL-6 cytokine responses induced by various stimuli. The framework used in this study may allow for the analysis of rare and common genetic variants in a wider variety of (non-immune) complex phenotypes and therefore has the potential to contribute to better understanding of unresolved, complex traits and diseases.
MeSH term(s)	Biomarkers ; Cytokines/genetics ; Cytokines/metabolism ; Disease Susceptibility ; Gene Expression Profiling ; Gene Expression Regulation ; Genetic Variation ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Immunity, Innate ; Immunophenotyping ; Inflammation/genetics ; Inflammation/metabolism ; Interleukin-1/genetics ; Interleukin-1/metabolism ; Interleukin-1beta ; Signal Transduction ; Systems Biology/methods
Chemical Substances	Biomarkers ; Cytokines ; Interleukin-1 ; Interleukin-1beta
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-021-00907-w
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Article ; Online: Human variation in population-wide gene expression data predicts gene perturbation phenotype.

Bonaguro, Lorenzo / Schulte-Schrepping, Jonas / Carraro, Caterina / Sun, Laura L / Reiz, Benedikt / Gemünd, Ioanna / Saglam, Adem / Rahmouni, Souad / Georges, Michel / Arts, Peer / Hoischen, Alexander / Joosten, Leo A B / van de Veerdonk, Frank L / Netea, Mihai G / Händler, Kristian / Mukherjee, Sach / Ulas, Thomas / Schultze, Joachim L / Aschenbrenner, Anna C

iScience

2022 Volume 25, Issue 11, Page(s) 105328

Abstract: Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function " ...

Abstract	Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function "
Language	English
Publishing date	2022-10-12
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.105328
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Article ; Online: Author Correction: Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death.

Byrne, Alicia B / Arts, Peer / Ha, Thuong T / Kassahn, Karin S / Pais, Lynn S / O'Donnell-Luria, Anne / Babic, Milena / Frank, Mahalia S B / Feng, Jinghua / Wang, Paul / Lawrence, David M / Eshraghi, Leila / Arriola, Luis / Toubia, John / Nguyen, Hung / McGillivray, George / Pinner, Jason / McKenzie, Fiona / Morrow, Rebecca /

Lipsett, Jill / Manton, Nick / Khong, T Yee / Moore, Lynette / Liebelt, Jan E / Schreiber, Andreas W / King-Smith, Sarah L / Hardy, Tristan S E / Jackson, Matilda R / Barnett, Christopher P / Scott, Hamish S

Nature medicine

2023 Volume 30, Issue 1, Page(s) 302

Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-023-02487-1
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Article ; Online: Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death.

Nature medicine

2023 Volume 29, Issue 1, Page(s) 180–189

Abstract: Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in ... ...

Abstract	Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in 105 families. Our cohort provides evidence of severe atypical in utero presentations of known genetic disorders and identifies novel phenotypes and disease genes. Inheritance of 42% of definitive diagnoses were either autosomal recessive (30.8%), X-linked recessive (3.8%) or autosomal dominant (excluding de novos, 7.7%), with risk of recurrence in future pregnancies. We report that at least ten families (5%) used their diagnosis for preimplantation (5) or prenatal diagnosis (5) of 12 pregnancies. We emphasize the clinical importance of genomic investigations of pregnancy loss and perinatal death, with short turnaround times for diagnostic reporting and followed by systematic research follow-up investigations. This approach has the potential to enable accurate counseling for future pregnancies.
MeSH term(s)	Pregnancy ; Humans ; Female ; Perinatal Death/etiology ; Autopsy ; Abortion, Spontaneous/genetics ; Prenatal Diagnosis ; Genomics
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-022-02142-1
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Article ; Online: Al-Gazali Skeletal Dysplasia Constitutes the Lethal End of ADAMTSL2-Related Disorders.

Batkovskyte, Dominyka / McKenzie, Fiona / Taylan, Fulya / Simsek-Kiper, Pelin Ozlem / Nikkel, Sarah M / Ohashi, Hirofumi / Stevenson, Roger E / Ha, Thuong / Cavalcanti, Denise P / Miyahara, Hiroyuki / Skinner, Steven A / Aguirre, Miguel A / Akçören, Zühal / Utine, Gulen Eda / Chiu, Tillie / Shimizu, Kenji / Hammarsjö, Anna / Boduroglu, Koray / Moore, Hannah W /

Louie, Raymond J / Arts, Peer / Merrihew, Allie N / Babic, Milena / Jackson, Matilda R / Papadogiannakis, Nikos / Lindstrand, Anna / Nordgren, Ann / Barnett, Christopher P / Scott, Hamish S / Chagin, Andrei S / Nishimura, Gen / Grigelioniene, Giedre

Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research

2023 Volume 38, Issue 5, Page(s) 692–706

Abstract: Lethal short-limb skeletal dysplasia Al-Gazali type (OMIM %601356), also called dysplastic cortical hyperostosis, Al-Gazali type, is an ultra-rare disorder previously reported in only three unrelated individuals. The genetic etiology for Al-Gazali ... ...

Abstract	Lethal short-limb skeletal dysplasia Al-Gazali type (OMIM %601356), also called dysplastic cortical hyperostosis, Al-Gazali type, is an ultra-rare disorder previously reported in only three unrelated individuals. The genetic etiology for Al-Gazali skeletal dysplasia has up until now been unknown. Through international collaborative efforts involving seven clinical centers worldwide, a cohort of nine patients with clinical and radiographic features consistent with short-limb skeletal dysplasia Al-Gazali type was collected. The affected individuals presented with moderate intrauterine growth restriction, relative macrocephaly, hypertrichosis, large anterior fontanelle, short neck, short and stiff limbs with small hands and feet, severe brachydactyly, and generalized bone sclerosis with mild platyspondyly. Biallelic disease-causing variants in ADAMTSL2 were detected using massively parallel sequencing (MPS) and Sanger sequencing techniques. Six individuals were compound heterozygous and one individual was homozygous for pathogenic variants in ADAMTSL2. In one of the families, pathogenic variants were detected in parental samples only. Overall, this study sheds light on the genetic cause of Al-Gazali skeletal dysplasia and identifies it as a semi-lethal part of the spectrum of ADAMTSL2-related disorders. Furthermore, we highlight the importance of meticulous analysis of the pseudogene region of ADAMTSL2 where disease-causing variants might be located. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
MeSH term(s)	Humans ; Bone Diseases, Developmental/genetics ; Limb Deformities, Congenital/genetics ; Limb Deformities, Congenital/pathology ; Osteochondrodysplasias/genetics ; Bone and Bones/pathology ; Homozygote ; ADAMTS Proteins/genetics
Chemical Substances	ADAMTSL2 protein, human (EC 3.4.24.-) ; ADAMTS Proteins (EC 3.4.24.-)
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632783-7
ISSN	1523-4681 ; 0884-0431
ISSN (online)	1523-4681
ISSN	0884-0431
DOI	10.1002/jbmr.4799
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