ESSENTIAL INFORMATION FORmcp.bs.jhmi.edu/sites/default/files/18 SBCAL BRayton 2... · 2018-06-14 · Blackthorn,England C Block B6.V‐Lepob/OlaHsd Absent Bresso, Italy Isolators

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AMAZING MICEESSENTIAL INFORMATION FOR

RESEARCH REPRODUCIBILITY AND VALIDITYCory Brayton, DVM, Diplomate, ACLAM, ACVP

Director, Phenotyping Core

Associate Professor, Molecular and Comparative Pathobiology

Johns Hopkins University, School of Medicine

733 North Broadway BRB 851

Baltimore, MD 21205

Co EIC ILAR Journal

[email protected]

Disclosures • No financial disclosures that I know of…• All opinions expressed and implied in this presentation are solely those of Dr. Brayton.

• The content of the presentation does NOT represent or reflect the views of Johns Hopkins University or Johns Hopkins Health system, or of ILAR or the National Academies.

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Guidelines, Guidance, Recommendations: For REPORTING/REVIEWING:

ARRIVE Guidelines; Kilkenny 2010 https://www.nc3rs.org.uk/sites/default/files/documents/Guidelines/NC3Rs%20ARRIVE%20Guidelines%20Checklist%20(fillable).pdf

ILAR guidance NRC 2011http://ilarjournal.oxfordjournals.org/content/55/3/536.full.pdf+html

NIH Principles and Guidelines for Reporting Preclinical Research 2014 http://www.nih.gov/research‐training/rigor‐reproducibility/principles‐guidelines‐reporting‐preclinical‐research

FASEB Recommendations 2016 Enhancing Research Reproducibility https://www.faseb.org/Portals/2/PDFs/opa/2016/FASEB_Enhancing%20Research%20Reproducibility.pdf

etc4

20 areas of a research manuscript (ARRIVE Guidelines)

• https://www.nc3rs.org.uk/arrive‐guidelines.5

Specialty group guidance Minimum information recommendations: e.g. MinPDX, MinPEPa (pathology), MinSC (stem cells)…

Trends in author/reviewer check lists e.g. Nature, Gold Standard, etc.

PROTOCOL Resource/repository https://www.protocols.io/ Find, discuss, implement, report, revise protocols, ‘publish’ with DOI

For study DESIGN: Smith et al. (2017). PREPARE: guidelines for planning animal research and testing. Lab Anim als. http://journals.sagepub.com/doi/abs/10.1177/0023677217724823?url_ver=Z39.88‐2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed

Additional Guidance, Tools:

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18 SBCAL Brayton 2 Amazing Mice

[email protected] 2018 Page 1 of 11

Betteranimal and

human healthWhat we Need?

(Time / $$$)

Tools for better reporting

Education

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Means to an end … (Part of a strategy to achieve better science for better health and well being )

Problem/Concern: Current research is NOT sufficiently Reproducible to achieve scientific aims.

Hypothesis: Improved reproducibility thru Rigorous Robust Relevant research design and reporting will improve validity, & human & animal health…

Corollary Animal welfare & well being (3R’s) is good for research …

Is Reproducibility the real goal?

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NEXT STEPS? TODAY, now:• Understanding mouse names Reporting mice accurately in Materials and Methods of Your NEXT paper…

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AIMS

• Better understanding of MICE and their NAMES for• Better EXPERIMENTAL DESIGN and REPORTING for• Better RESEARCH REPRODUCIBILITY and VALIDITY for• Better human and animal HEALTH

Betteranimal and human health

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[NRC] National Research Council. ILAR. 2011.

Guidance for the Description of Animal Research in Scientific Publications. Washington, DC: National Academies Press.

• Available online (http://www.nap.edu/catalog.php?record_id=13241 or https://www.ncbi.nlm.nih.gov/pubmed/22379656),

ILAR GUIDANCE (NRC 2011)

• Regarding Materials and Methods (M&M)– Background strain:

• …The use of shortened stock and strain designations (e.g., Sprague‐Dawley rat or C57BL mouse) instead of the fully defined genetic nomenclature is not appropriate in published animal descriptions….

– Microbial status:• …list of the pathogens excluded, reference to the pathogen exclusion

list from the commercial supplier…..

• With Scientific justifications and references….. 11

Different from‘The Guide’

• ‘THE Guide’ for the care and use of laboratory animals:

• 8th Ed, NRC 2011 BUT Relevant themes: …created by scientists and veterinarians for scientists and veterinarians to uphold the scientific rigor and integrity of biomedical research with laboratory animals as expected by their colleagues and society at large….

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20 areas of a research manuscript (ARRIVE Guidelines)

• https://www.nc3rs.org.uk/arrive‐guidelines.13

• The animal(s) Strain, substrain(name, including relevant genotypes)

Sex(es) o Justify the use of only 1 sex, if applicable

Age(s) n (#) (justified by statistics Etc: parity, microbial status……

Re Reporting :

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C57BL/6 (‘B6’)

Important/famous for: • 1st Mouse Genome project: C57BL/6J• ES cells for IKMC: C57BL/6N• Low cancer• Disease resistance i.e. the mice that didn’t die ….

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Some B6 Phenotypes:• Black, non agouti a/a• Hydrocephalus (big ventricles) • Microphthalmia• Ulcerative dermatitis • Big thymus

stress susceptible?

• Small adrenals• Acidophilic macrophage pneumonia• Amyloidosis, reactive + senile • Osteoporosis• Portal systemic shunts (J)• Cerebral vascular variations

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Atherosclerosis Like drugs & alcohol Dz resistance Lo tumor strain but:

Lymphoma, Histiocytic sarcoma, esp in F

C58 – thymic lymphomaC57BL/Ks ‐ hydronephrosis

Some B6 genotypesGeneallele Gene , allele info System /phenotype

a/a a/a Black non agouti

H2 b MHC haplotype Immunity

Ahrb‐1 aryl‐hydrocarbon receptor B1 variant (immune) etc

Apoa2a Apolipoprotein A2 a allele Less? Senile amyloid

Cdh23ahl cadherin 23 age related hearing loss 1 Hearing

Slc11a1s solute carrier family 11 (Nramp1) susceptible Immunity

Some Genes with variations among J and N substrainsAanat arylalkylamine N‐acetyltransferase ( lo melatonin) Endocrine/Pineal

Dock2 dedicator of cyto‐kinesis 2 Immunity

Nlrp12 NLR protein 12 Immunity

Nnt nicotinamide nucleotide transhydrogenase deficient Gluc Metabolism

Snca Alpha synuclein 1 point mutation CNS/neuro

Crb1rd8 crumbs homolog 1; retinal degeneration 8 vision

Summarized from MGI/IMSR etc

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Lots of ‘B6’

C57BL/6NCr =

C57BL/6By C57BL/6ByJ

C57BL/6JBailey N UCSF J

adapted from http://www.envigo.com/

• Expect genotype variations

• Expect phenotype variations

• Which do you use?• WHY?

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B6 History – another version

• Mekada et al. 2015

• 11 C57BL/6Nsubstrains

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B6 substrain options..Substrain Source

C57BL/6J C57BL/6J The Jackson Laboratory via CRL Japan, Inc. (Yokohama, Japan)C57BL/6JJcl CLEA Japan Inc. (Tokyo, Japan)C57BL/6JJmsSlc Japan SLC, Inc. (Hamamatsu, Japan)C57BL/6JEiJ The Jackson Laboratory (Bar Harbor, MA, USA)C57BL/6JOlaHsd Harlan Laboratories, Inc. (Indianapolus, IN, USA)C57BL/6JRccHsd Harlan Laboratories, Inc. (Indianapolus, IN, USA)C57BL/6JBomTac Taconic Farm Inc. (New York, NY, USA)

C57BL/6N C57BL/6NJ The Jackson Laboratory (Bar Harbor, ME, USA)C57BL/6NCrSim Simonsen Laboratories, Inc. (Gilroy, CA, USA)C57BL/6NTac Taconic Farm Inc. (New York, NY, USA)C57BL/6NJcl CLEA Japan Inc. (Tokyo, Japan)C57BL/6NSeac Kyudo Co. Ltd. (Tosu, Japan)C57BL/6NCrlCrlj Charls River Laboratories Japan, Inc. (Yokohama, Japan)C57BL/6NCrl Charles River Laboratories International, Inc. (Wilmington, MA, USA)C57BL/6NHsd Harlan Laboratories, Inc. (Indianapolis, IN, USA)C57BL/6NCrSlc Japan SLC, Inc. (Hamamatsu, Japan)C57BL/6By The Jackson Laboratory (Bar Harbor, MA, USA) ??C57BL/6ByJ The Jackson Laboratory (Bar Harbor, MA, USA)

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N

(a few) B6 SUBstrain variations B6 Substrain Source

(‐/‐)Dock2

(‐/‐)Nlrp12

(‐/‐)Nnt

(‐/‐)Snca

(‐/‐)Mmrn1

(‐/‐)Rd8

C57BL/6J Jackson No YES YES No No No

C57BL/6J * Charles Riv NP NP YES No No No

C57BL/6JOlaHsd Hsd/Envigo NP NP No YES YES No

C57BL/6JRccHsd Hsd/Envigo NP NP No No No No

C57BL/6JBomTac Taconic NP NP No No No No

C57BL/6JRj Janvier NP NP NP NP NP NP

C57BL/6ByJ Jackson No NP No No No No

C57BL/6NHsd Hsd/Envigo SOME NP No No No YES

C57BL/6NRj Janvier No NP NP NP NP NP

C57BL/6NCrl Charles Riv No NP No No No YES

C57BL/6NTac Taconic No NP No No No YES

C57BL/6NCr NCI NP No NP NP NP NP

Adapted/updated from envigo.com 2015 * J mice distributed by Crl in EU NP = not published

J

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(a few) B6 SUBstrain variations

Hypomorphic spontaneous mutations Dock2 dedicator of cyto‐kinesis 2; migration of T and B lympohcytes;

response to chemokines (Nlrp12 NLR family, pyrin domain containing 12; innate immunity,

neutrophil recruitment, dendritic and myeloid cell migration Nnt nicotinamide nucleotide transhydrogenase; encodes an integral

protein of the inner mitochondrial membrane, associated with metabolic phenotypes

Snca alpha synuclein; in a family of related proteins expressed in brain (protein in Lewy body inclusions, implicated in Parkinson’s Dz). Deletion includes Mmrn1 multimerin 1; a stored platelet and

endothelial cell adhesive protein.

Rd8 retinal degeneration 8; single base pair mutation in the CRB1 gene (a gene linked to macular degeneration in humans)

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Location Building Strain Dock2hsd PCR Results Indianapolis, IN 202A C57BL/6NHsd Absent Indianapolis, IN 202C C57BL/6NHsd C57BL/6BrdCrHsd‐Tyrc Absent Indianapolis, IN 217 C57BL/6NHsd B6.V‐Lepob/OlaHsd Absent Haslett, MI 206 C57BL/6NHsd Present repopulated 2017/8Frederick, MD 208 C57BL/6NHsd Present repopulated 2017/8Houston, TX* 211 C57BL/6NHsd Absent Dublin, VA 231 C57BL/6NHsd CB6F1/Hsd B6C3F1/Hsd B6D2F1/Hsd Present repopulated 2017/8Livermore, CA 237 C57BL/6NHsd Absent Mexico City, Mexico 650 C57BL/6NHsd Present repopulated 2017/8Gannat, France Isolators C57BL/6JOlaHsd C57BL/6JRccHsd B6.V‐Lepob/OlaHsd Absent

Horst, Netherlands Barrier 2 C57BL/6JOlaHsd C57BL/6JRccHsd Absent

Horst, Netherlands Barrier 2 C57BL/6NHsd Present Rehovot, Israel 640 C57BL/6JOlaHsd C57BL/6JRccHsd Absent

Jerusalem, Israel 610 C57BL/6JOlaHsd Absent Udine, Italy 700W C57BL/6JOlaHsd, C57BL/6JRccHsd Absent Udine, Italy 700E C57BL/6JOlaHsd Absent Blackthorn, England C Block B6.V‐Lepob/OlaHsd Absent Bresso, Italy Isolators C57BL/6JOlaHsd C57BL/6JRccHsd Absent Bresso, Italy Isolators C57BL/6NHsd Present repopulated 2017/8Seoul, Korea N/A C57BL/6NHsd Results pending Borchen, Germany* Winkelmann C57BL/6NHsd Results pending Tests were conducted on foundation colony breeding cages. Genetic testing was performed at the Envigo Genetic Testing laboratories in Piscataway, NJ using qPCR technology. *Facility closed prior to 2016

Dock2 – Envigo B6 Colonies 6/9/16

Concerning that mice with same name C57BL/6NHsd may or may NOT carry the mutation ?

arose >20y ago…23

B6substrain variation


• 11 C57BL/6Nsubstrains

• 100 SNP loci

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B6NVariations

1) N cryoJ 20052) NCr Sim 19953) N Tac 19914) N JCI 19885) N Seac 19816) N CrlCrlJ 19767) N Crl 19748) N HSD 19749) N 1972 Slc 197410) N By 196111) N ByJ 1961

• J


Useful B6 references • Zurita et al. 2010. Genetic polymorphisms among C57BL/6 mouse inbred strains. Transgenic Res.

• Simon & al. 2013. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

• Kraev. 2014. Parallel universes of Black Six biology.• Mekada et al. 2015. Development of SNP markers for C57BL/6N‐derived mouse inbred strains.

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• Abolins et al. 2017. The comparative immunology of wild and laboratory mice, Mus musculus domesticus. Nature. B6 vs wild mice (& humans) …

• Beura et al. 2016. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature. B6 vs pet store mice (& humans)….

• Seok et al. 2013. Genomic responses in mouse models poorly mimic human inflammatory diseases. PNAS. Takao & Miyakawa. 2015. Genomic responses in mouse models greatly mimic human inflammatory diseases. PNAS. (Same Data)

B6 representing all mice vs human…

B6 represent ALLlaboratory mice ?

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WILDA, BALB, C3

DBA

129

C57, C58Group 1: Bagg albino derivativesGroup 2: SwissGroup 3: Japanese &

New Zealand inbredGroup 4: Abbie Lathrop’s

C57/58Group 5: Castle's 129 etcGroup 6: CC Little's

DBA & relatedGroup 7: wild‐derived

B6 do NOT represent all Lab mice.

Petkov et al 2004. An efficient SNP system for mouse genome scanning elucidating strain relationships. Genome Res. 2004 Sep;14(9):1806‐11.

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NEXT:

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BALB/c…..• Famous For Monoclonal Antibodies Used to study Infectious Disease

• Likely Killers (CoD = Cause of Death) Each other – esp males Heart disease, diverse tumors

• Also see Acallosity; Cardiac calcinosis, Thrombi, Cardiomyopathy; Vaginal septa, imperforate vagina, poor fertility

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BALB/c more than other strains ?

Cardiac Conditions • Epicardial mineralization Right Ventricle (RVFW)

• Thrombi left atrium

• ‘Cardiomyopathy’ Inflammation Degeneration Fibrosis

Miscellaneous Tumors• Plasma cell myeloma Monoclonal AB

• Rhabdomyosarcoma• Salivary Myoepithelioma

• Mammary • Harderian gland• Adrenal cortical • Thyroid

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1937 1937/81938/9

1913

1947

A short history of BALB/c Family tree (Pedigree) of Bagg’s albino mice

• Which do you use? • Why?

Andervont

N strains

ScottJ

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BALB/c killer males?• ….Scott did not select or purposely breed BALB/c mice for aggressive behavior ….In 1942 he notes that weanling BALB/c males could be housed 5 to a cage ... Further BALB/c albinos became lethargic in warm weather.

• …These observations put us at a loss to explain why BALB/cJ males are viciously aggressive when compared with their docile BALB/cAn ….

From Potter 1985. History of the BALB/c Family• https://link.springer.com/chapter/10.1007/978‐3‐642‐70740‐7_1

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BALB/c substrain options

AndervontBALB/cAn BALB/cAnBy Bailey

o BALB/cByJ

BALB/cAnN NIHo BALB/cAnNCrlo BALB/cNHsdo BALB/cAnNTac

BALB/cAnHe Heston

• Scott J• BALB/cJ BALB/cJBomTac BALB/cOlaHsd

♦ More – BUT not so available, e.g. – BALB/cWtEiJ

Separated c 1932 ~F26

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Some BALB/c genotypes

Strains Geneallele Gene , allele info System or phenotype

BALB/cByJBALB/cJ

c/c A/A Tyrp1b/Tyrp1b Tyrc/Tyrc albino

H2 d MHC haplotype immune

Hld hippocampal lamination defect Brain

Apoa2b Apolipoprotein A2 – b variant (Hdlq5) Hier HDL (lo ASSAM)

BALB/cByJBALB/cAnEtc?

Prkdcbalb/cprotein kinase, DNA activated, catalytic polypeptide (Balb/c allele has less effect than scid)

IMMUNEradiosensitivity etc

BALB/cByJ Acadsdel‐J acyl‐Coenzyme A dehydrogenase deficiency organic aciduria

BALB/cByJ Ahrb‐2 aryl‐hydrocarbon receptor B2 variant Immunity

BALB/cByJ Cdh23ahl cadherin 23 (otocadherin) age related hearing loss 1 Hearing

BALB/cByJ Mdmg1 mandibular morphogenesis 1 longer dorsal edge Skeletal

From http://www.findmice.org/IMSRSearchForm.jsp etc35

B6 vs BALB/c immunity oversimplified

B6 BALB/cH2 b H2 d

TH1 bias IL12 TH2 bias IL4More cell mediated More humoral responseIntermediate ‐Hi NK activity (Ly49)Specific Klr NK complex

Intermediate ‐less NK activity

More macrophage activity , TNFa, IL12, bacterial killing; more local/less systemic response

Less macrophage activity, TNFa, IL12, bacterial killing; more systemic & acute phase response

B6J / B6N variation in Th17response

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Another example…

• …gene mutation causing complete unresponsiveness [to LPS] occurred after 1960 and by 1968 was inbred into the C3H/HeJ colony… Glode & Rosenstreich 1976.

https://www.ncbi.nlm.nih.gov/pubmed/792337

C3H…. & the story of Tlr4lps

C3H/StC3H/CrC3H/BiC3H/HeC3H/HeNC3H/HeJC3H/HeBFeJC3H/DiSnC3H/AvyC3H/Bts

Fire Jax

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Another Spontaneous Tlr4mutation

Tlr4lps‐del

• In C57BL/10ScNJ

• (C57BL/10ScCr) Poltorak et al. (1998).

• (C57BL/10Cr) Coutinho & Meo (1978).

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STRAIN MATTERS.Phenotypes in ‘Normal’? (+/+) Mice129? Teratomas (Ter), lung tumors, acallosity, AMP, …

A/J Lung tumors, anomalies, amyloid, muscular dystrophy

AKR Thymic Lymphoma…

BALB/c Plasmacytoma etc tumors, heart dz, acallosity, kill each other

C3H TUMORS ‐Mammary, Liver

C57BL/6 Microphthalmia, Hydrocephalus , MUD, Osteoporosis, Presbyacusis, Amyloidosis, AMP, …

DBA Deaf, seizures, glaucoma, autoimmune

FVB/N? Blind, seizures, mammary/pituitary dz

NOD Diabetes, immunoweird

SJL/J Lymphoma, muscular dystrophy, kill each other

DEAF C57BL/6, BALB, DBA, etc

BLIND rd1 C3H, CBA, SJL, SWR, FVB

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Plenty of Deaf and or Blind mice …

• Vision/Hearing are not so important to mice

• Vibrissae are important

• Olfactory is important

• ZEMBRZYCKI ET AL. NATURE NEUROSCIENCE, 201340

SEX MATTERS too.

• Prevalence of sexual dimorphism in mammalian phenotypic traits. Nat Commun. 2017 Jun 26;8:15475. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490203/ How many authors does it take to convince a scientist?

• Karp et al: Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez‐Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL; International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK. +159 Collaborators: bata Y, Suzuki T, Tamura M, Kaneda H, Furuse T, Kobayashi K, Miura I, Yamada I, Tanaka N, Yoshiki A, Ayabe S, Clary DA, Tolentino HA, Schuchbauer MA, Tolentino T, Aprile JA, Pedroia SM, Kelsey L, Vukobradovic I, Berberovic Z, Owen C, Qu D, Guo R, Newbigging S, Morikawa L, Law N, Shang X, Feugas P, Wang Y, EskandarianM, Zhu Y, Nutter LMJ, Penton P, Laurin V, Clarke S, Lan Q, Sohel K, Miller D, Clark G, Hunter J, Cabezas J, Bubshait M, Carroll T, Tondat S, MacMaster S, Pereira M, Gertsenstein M, Danisment O, Jacob E, Creighton A, Sleep G, Clark J, Teboul L, Fray M, Caulder A, Loeffler J, Codner G, Cleak J, Johnson S, Szoke‐Kovacs Z, Radage A, Maritati M, Mianne J, Gardiner W, Allen S, Cater H, Stewart M, Keskivali‐Bond P, Sinclair C, Brown E, Doe B, Wardle‐Jones H, Grau E, Griggs N, Woods M, Kundi H, Griffiths MND, Kipp C, DT, Vancollie VE, Pearson SA, Gates AS, Sanderson M, Shannon C, Anthony LFE, Sumowski MT, McLaren RSB, Swiatkowska A, Isherwood CM, Cambridge EL, Wilson HM, Caetano SS, Mazzeo CI, Dabrowska MH, Lillistone C, Estabel J, Maguire AKB, Roberson LA, Pavlovic G, Birling MC, Marie WD, Jacquot S, Ayadi A, Ali‐Hadji D, Charles P, André P, Le MarchandE, El Amri A, Vasseur L, Aguilar‐Pimentel A, Becker L, Treise I, Moreth K, Stoeger T, Amarie OV, Neff F, Wurst W, Bekeredjian R, Ollert M, Klopstock T, Calzada‐Wack J, Marschall S, Brommage R, Steinkamp R, Lengger C, Östereicher MA, Maier H, Stoeger C, Leuchtenberger S, Yildrim A, Garrett L, Hölter SM, Zimprich A, Seisenberger C, Bürger A, Graw J, Eickelberg O, Zimmer A, Wolf E, Busch DH, Klingenspor M, Schmidt‐Weber C, Gailus‐Durner V, Beckers J, Rathkolb B, Rozman J. Melvin DG, Raj NPS, Holroyd SA, Gannon DJ, Alcantara R, Galli A, Hooks YE, Tudor CL, Green AL, Kussy FL, Tuck EJ, Siragher EJ, Maguire SA, Lafont 41

Mice/Names•CONCLUSIONS: Strain matters. Sex matters. Beware of incomplete or inaccurate names… Be aware of nomenclature …

Final Exam : (Your research!)o WHY do you use a specific strain or substrain?o Relevant phenotypes/genotypes to your research?o Would other strains be useful to your research?

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Nomenclature – mission critical in scientific communication…

• Correct strain names identify strain(s) of origin, and where it has been, and came from

• Correct mutant names tell a lot about the mice & mutations

• Incorrect names compromise communication, reproducibility, translational research

USE CORRECT NAMES. REQUIRE CORRECT NAMES when reviewing & editing. Get a Lab Code if you make or breed mice Its FREE $ & EASY! USE THIS SITE:http://www.informatics.jax.org/mgihome/nomen/index.shtml

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Strain First - Genotype/Laboratory codes

• B6.129P2-Apoa1tm1Unc/J

• B6.I29P2-ApoaItmIUnc/J

• B6;129X1-Apoa5tm1Lap Apoc3tm1Lap

• B6;I29XI-Apoa5tmILap Apoc3tmILap

• B6;CBA-Tg(APOC1)1Bres/J

• B6;CBA-Tg(APOCI)IBres/J

Inbred Strain Nomenclature

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Background strain(s) ?Congenic ? Mutation strategy ?Inserted gene(s) ?Disrupted gene(s)? Who made it? Where is it available ?

USE THIS SITE (+TUTORIAL):http://www.informatics.jax.org/mgihome/nomen/index.shtml

Outbred Nomenclature

• Source (lab code 1st) Lab code: STOCK name(etc info) e.g.

CRL:CD-1®(ICR)BRCRL:CFW®(SW) BR CRL:CF-1® BR (NOT Swiss)Cr:NGP(S)Cr:NIH(S)

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Br = barrier rearedcc = closed colony

Hsd:ICR(CD-1®)Hsd:ND4Hsd:NIHS IcrTac:ICR Tac:SWBomTac:NMRI

USE THIS SITE (+TUTORIAL):http://www.informatics.jax.org/mgihome/nomen/index.shtml

WILDA, BALB, C3

DBA

129

C57, C58

What strain to represent ALL mice (& humans)?Group 1: Bagg albino derivativesGroup 2: SwissGroup 3: Japanese &

New Zealand inbredGroup 4: Abbie Lathrop’s

C57/58Group 5: Castle's 129 etcGroup 6: CC Little's

DBA & relatedGroup 7: wild‐derived 46

Petkov et al 2004. An efficient SNP system for mouse genome scanning elucidating strain relationships. Genome Res. 2004

• ‘genetically undefined’ vs ‘outbred’

Not inbred but also Famous..

abbrev origin

CD1 Swiss

ICR Swiss

ND4 Swiss

NMRI Swiss

Swiss Swiss

SW (Swiss Webster) Swiss

[CC Collaborative Cross (8 strains ) RI strains]

DO CC RI (Recombinant Inbreds)

4WC, Het Other heterogeneous stocks

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INcompleteness of background strain reporting in recent publications

Background strain notation 2010 2011 2012 2013 2014 Combined totals or averages

Completely addressed 54 56 49 52 43 Combined total: 254

Incompletely addressed 77 64 55 86 80 Combined total: 362

Incomplete due to C57BL/6 43 43 40 52 48 Combined total: 226

Total number of articles 126 123 105 138 124 Combined total: 616

% incomplete total 61 52 52 62 64.5 Average: 58.5% of incompletes due to C57BL/6 56 67 73 60.5 60 Average: 63

Fontaine & Davis 2016. Diabetes. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4686949 /



Recent Headline

• Better research & reporting is up to YOU!!!

MICE STRAINS

Tomorrow’s Headline

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Conclusions• Use the Guidance Expect Journals to require relevant and accurate detail about animals and research conditions.

• Names, Strains (& substrains) are important All mice are not the same (and not B6!) Strain genetics and phenotypes are important in our research.

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• Find Gene info & correct/current names (MGI) http://www.informatics.jax.org/genes.shtml http://www.informatics.jax.org/mgihome/nomen/index.shtml (with nomenclature tutorial)

• More on strains/phenotypes https://phenome.jax.org/projects/Brayton1

• Mouse Pathobiology & Phenotyping Course & Lab manual (free to download) http://mcp.bs.jhmi.edu/me680712‐phenotyping‐functional‐genetics

**Resources** (Mice)

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RESOURCES: Find GEM(Genetically Engineered Mice) • IMSR – Induced Mutant Strain Resource Database find mice in multiple resources http://www.findmice.org/index.jsp

• IKMC – International Knockout Mouse Consortium (and repositories) http://www.mousephenotype.org/ (IMPC)

• EMMA – European Mutant Mouse Archive• MMRRC – Mutant Mouse Research Resource Centers (c 1998)

• RIKEN ‐ Japan

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• Mouse Phenome Database (MPD) Emphasizing J strains; protocol detail; published studies; http://phenome.jax.org/

• EUROPHENOME GEM – IMPRESS (EMPRESS) protocols as applied in EUMODIC = European mouse disease clinics http://www.europhenome.org/

• CA – NorComm http://www.norcomm.org• J – RIKEN BRC Japan Mouse Clinic http://www.brc.riken.jp/lab/jmc/mouse_clinic/en/

RESOURCES: Find Phenotype Data and Protocols (Mice)

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• For REPORTING (publishing) Animal Research: NIH.gov ‐ summary list (incomplete)

o https://www.nlm.nih.gov/services/research_report_guide.html

ARRIVE guidelines – Kilkenny & al 2010 – NC3R’s o https://www.ncbi.nlm.nih.gov/pubmed/20613859

ILAR/NAS guidance for reporting (NRC 2011)o http://www.nap.edu/catalog.php?record_id=13241

FASEB Recommendations 2016 o https://www.faseb.org/Portals/2/PDFs/opa/2016/FASEB_Enhancing%20Research%20Reproducibility.pdf

RESOURCES: (Guidelines)

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• For PROTOCOLS and PLANNING studies Protocols.io: Virtual Communities for Protocol Development and Discussion. Teytelman et al. 2016.

o https://www.ncbi.nlm.nih.gov/pubmed/27547938o Find, discuss, implement, report, revise protocols, ‘publish’ with DOI https://www.protocols.io/

PREPARE: Guidelines for planning animal research and testing. Smith et al. 2017.

o https://www.ncbi.nlm.nih.gov/pubmed/28771074

RESOURCES: (Other)

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Headlines:

•We CAN do better.

https://www.the‐scientist.com

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Thanks!! Obrigado!! • Hosts !!• Audience !!• Mice & GEM• Nadine Forbes• MCP & core faculty• LAM & Vet path trainees NIH T32 RR0077022

That’s all folks!

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Where are we now ?(in terms research reproducibility)

What we have : (Survey ‘data’)

Guidelines Recommendations

Concerns, Complaints, POOR Reproducibility, POOR reporting….

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Betteranimal and

human health

What we learned from a 2017 Survey onExternal Environmental factors

• 180 responses as of 10/14/17 (AALAS)• Average response time ~ 5min • Compmed, MGI list, institutional list serves, colleagues ….

• Not a perfect survey • But pretty quick • Interesting:

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Q 1: WHO responded

• 175 responses• 5 skipped• 14 comments addl roles IACUC staff Lab manager QA head Post doc funder

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53% Researcher / Faculty Scientists



Q 4: which.. factors can affect rigor and reproducibility?

…(infectious agents and microbiome were NOT included)• 174 responded 60‐90% for All categories

• 6 skipped• 34 ‘other’ All NOISE Vibration Personnel Microbiota Fasting/Fed

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Q 5: What do you think is important ?• 156 responses

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(‘word cloud’ from the responses)

Q7: DO YOU see need to increase reporting of extrinsic environmental factors …

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Q7: DO YOU see need to increase reporting of extrinsic environmental factors ..

• Answered: 175• Skipped: 5

• 20 comments

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Overwhelming Majority:YES its important BUT…

• we need mechanisms to facilitate collecting and reporting (69%}

• it does not seem necessary to publish or to get grants (41%)

DISCLAIMER(s)/Disclosures• This presentation reflects MY (conscious and unconscious) biases that some thing(s) should be done to improve research reproducibility and validity….

• The content does NOT represent or reflect the views of Johns Hopkins University or Johns Hopkins Health system, or of ILAR or the National Academies.

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What is our ??

• Research reproducibility?

• Animal welfare?• Less animal research?• No animal research?• Improved animal and human health?

...via better reproducibility, data validity, and more predictive outcomes ……

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Documents

ESSENTIAL INFORMATION FORmcp.bs.jhmi.edu/sites/default/files/18 SBCAL BRayton 2... · 2018-06-14 · Blackthorn,England C Block B6.V‐Lepob/OlaHsd Absent Bresso, Italy Isolators