Commit e3b958d2 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'doc/credits' into 'dev'

Doc/credits

Closes #4131

See merge request !697
parents 131363ed e840eb7f
Pipeline #146969 failed with stages
in 3 minutes and 37 seconds
......@@ -90,44 +90,89 @@ BMC Genomics 2014, 15:409
Jean-Sebastien Allain et al.,
*IGHV segment utilization in immunoglobulin gene rearrangement differentiates patients with anti-myelin-associated glycoprotein neuropathy from others immunoglobulin M-gammopathies*,
Haematologica, 2018, 103:e207-e210
http://dx.doi.org/10.3324/haematol.2017.177444
<http://dx.doi.org/10.3324/haematol.2017.177444>
Jack Bartram et al.,
*High throughput sequencing in acute lymphoblastic leukemia reveals clonal architecture of central nervous system and bone marrow compartments*
Haematologica, 2018,
<https://dx.doi.org/10.3324%2Fhaematol.2017.174987>
Sébastien Bender et al.,
*Immunoglobulin variable domain high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome*
Blood, 2020,
<https://doi.org/10.1182/blood.2019004197>
Yann Ferret et al.,
*Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis*,
British Journal of Haematology, 2016, 173, 413–420
https://hal.archives-ouvertes.fr/hal-01279160
<https://hal.archives-ouvertes.fr/hal-01279160>
Henrike J. Fischer et al.,
*Modulation of CNS autoimmune responses by CD8+ T cells coincides with their oligoclonal expansion*
Journal of Neuroimmunology, 2015, S0165-5728(15)30065-5
http://dx.doi.org/10.1016/j.jneuroim.2015.10.020
<http://dx.doi.org/10.1016/j.jneuroim.2015.10.020>
Irene Jo et al.,
*Considerations for monitoring minimal residual disease using immunoglobulin clonality in patients with precursor B-cell lymphoblastic leukemia*,
Clinica Chimica Acta, 2019,
<https://doi.org/10.1016/j.cca.2018.10.037>
Takashi Kanamori et al.,
*Genomic analysis of multiple myeloma using targeted capture sequencing in the Japanese cohort*
British Journal of Haematology, 2020,
<https://doi.org/10.1111/bjh.16720>
Kenji Kimura et al.,
*Identification of Clonal Immunoglobulin λ Light-Chain Gene Rearrangements in AL Amyloidosis Using Next Generation Sequencing*,
ASH 2019,
<https://doi.org/10.1182/blood-2019-125028>
Michaela Kotrova et al.,
*The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL*,
Blood, 2015, 126:1045-1047
http://dx.doi.org/10.1182/blood-2015-07-655159
<http://dx.doi.org/10.1182/blood-2015-07-655159>
Michaela Kotrova et al.,
*Next‐generation amplicon TRB locus sequencing can overcome limitations of flow‐cytometric Vβ expression analysis and confirms clonality in all T‐cell prolymphocytic leukemia cases*,
Cytometry Part A, 93(11):1118-1124, 2018
http://dx.doi.org/10.1002/cyto.a.23604
<http://dx.doi.org/10.1002/cyto.a.23604>
Ralf A. Linker et al.,
*Thymocyte-derived BDNF influences T-cell maturation at the DN3/DN4 transition stage*
European Journal of Immunology, 2015, 45, 1326-1338
http://dx.doi.org/10.1002/eji.201444985
<http://dx.doi.org/10.1002/eji.201444985>
Edit Porpaczy et al.,
*Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy*,
Blood, 2018,
<https://dx.doi.org/10.1182/blood-2017-10-810739>
Mikaël Salson et al.,
*High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones*,
Leukemia Research, 2017, 53, 1–7
http://dx.doi.org/10.1016/j.leukres.2016.11.009
<http://dx.doi.org/10.1016/j.leukres.2016.11.009>
Florian Scherer et al.,
*Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA*,
Science Translational Medicine, 2016, 8, 364ra155
http://dx.doi.org/10.1126/scitranslmed.aai8545
Edit Porpaczy et al.,
*Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy*,
Blood, 2018,
https://dx.doi.org/10.1182/blood-2017-10-810739
<http://dx.doi.org/10.1126/scitranslmed.aai8545>
Udo zur Stadt et al.,
*Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL*
Blood Cancer Journal, 2019,
<https://doi.org/10.1038/s41408-019-0257-x>
Lucia Stranavova et al.,
*Heterologous Cytomegalovirus and Allo-Reactivity by Shared T Cell Receptor Repertoire in Kidney Transplantation*
Frontiers in Immunology, 2019,
<https://doi.org/10.3389/fimmu.2019.02549>
Gary Wright et al.,
*Clinical benefit of a high‐throughput sequencing approach for minimal residual disease in acute lymphoblastic leukemia*,
Pediatric Blood & Cancer, 2019,
<https://doi.org/10.1002/pbc.27787>
Wen‐Qing Yao et al.,
*Angioimmunoblastic T‐cell lymphoma contains multiple clonal T‐cell populations derived from a common TET2 mutant progenitor cell*
The Journal of Pathology, 2019,
<https://doi.org/10.1002/path.5376>
......@@ -34,7 +34,7 @@ and quantify immune recombinations.
- Many studies are still successfully using primer sets based on
the older **EuroClonality/BIOMED-2** sets
published in [(van Dongen, 2003)](http://dx.doi.org/10.1038/sj.leu.2403202).
See for example (Ferret, 2016)](https://hal.archives-ouvertes.fr/hal-01279160)
See for example [(Ferret, 2016)](http://dx.doi.org/10.1111/bjh.13981)
(1-step, 23 primers in 5 tubes, TRG, TRD/TRD+, IGK, IGK+).
These primer sets were designed and evaluated for onco-hematological studies on lymphoma and/or leukemia samples
......
......@@ -13,7 +13,7 @@ of any software doing immune repertoire sequencing (RepSeq) analysis.
Users and developers of RepSeq software are encouraged to [send us](contact@vidjil.org)
their manually curated sequences, ideally in the format described below, or by
directly proposing pull requests on Gitlab with new tests in the [`algo/tests/should-vdj`](https://gitlab.com/vidjil/vidjil/tree/master/algo/tests/should-vdj-tests) directory.
directly proposing pull requests on Gitlab with new tests in the [`algo/tests/should-vdj`](https://gitlab.inria.fr/vidjil/vidjil/tree/master/algo/tests/should-vdj-tests) directory.
We can also help to encode sequences in this format.
The current tests were contributed by:
......
......@@ -21,6 +21,8 @@ STATUS = {
True: 'ok'
}
USER_AGENT = {'User-Agent': 'Mozilla/5.0'}
stats = defaultdict(int)
failed = []
......@@ -36,7 +38,7 @@ def check_url(url, ids=[]):
# External http(s) links
try:
req = requests.get(url)
req = requests.get(url, headers = USER_AGENT)
return (req.status_code < 400)
except:
return False
......
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