Whole genome sequencing in paediatric channelopathy and cardiomyopathy

PMID: 38586174 Gene: MYBPC3 HGNC ID: 7551

PMID 37498360

Gene: TPM1

HGNC ID: 12010

Chronic Activation of Tubulin Tyrosination Improves Heart Function

PMID: 39279670 Gene: MYBPC3 HGNC ID: 7551

Hydroxychloroquine Cardiotoxicity and Sarcomeric Hypertrophic Cardiomyopathy.”

PMID: 40514126 Gene: MYBPC3 HGNC ID: 7551

Case#: 51-year-old Spanish man

DiseaseAssertion: Hypertrophic cardiomyopathy

FamilyInfo: Familial HCM

ParentalTesting:

CasePresentingHPOs: Hypertrophic cardiomyopathy

CaseHPOFreeText: not reported

CaseNotHPOs: not reported

CaseNotHPOFreeText: not reported

CasePreviousTesting: not reported

Genotyping Method: Genetic testing/sequencing

FunctionalAnalysis:

Variant: g.47363647G>A, p.Ala562Val

ClinVar: not found

CAID: CA078267

gnomAD: not found

AdditionalInfo: not reported

PMID: 32453731

Gene: MYL2

HGNC ID: 7583

Case1: Male, Infant, Tunisian

DiseaseAssertion: infantile-onset HCM and mitral valve dysplasia

FamilyInfo: Family with consanguinity in which four children had died before one year of age. The father (37 years old) and mother (27 years old) of the proband are consanguineously related. Two infants (VI:1 and VI:2) died at less than 30 days of age from cardiorespiratory arrest, and two (VI:3 and VI:4, proband) of them displayed abnormal cardiac findings on chest roentgenogram. While all four children displayed hepatomegaly and general hypotonia, VI:3 and VI:4 had a marked increase in heart size and died from refractory cardiogenic shock. The status of the MYL2 allele in siblings is unknown. The proband (fs/fs) was homozygous for the MYL2-fs allele while the parents were found to be heterozygous (fs/wt) carriers. The father (37 years old) and mother (27 years old) of the proband are consanguineously related, were asymptomatic from a cardiac standpoint and had normal cardiac anatomy and function as evaluated by an echocardiogram

ParentalTesting: Homozygous variant in the proband and that the parents are heterozygous carriers using Sanger DNA sequencing of the genomic region. Father (37 years old) and mother (27 years old) were asymptomatic from a cardiac standpoint and had normal cardiac anatomy and function as evaluated by an echocardiogram

CasePresentingHPOs: HP:0200128, HP:0001653, HP:0002092, HP:0001639, HP:0002240

CaseHPOFreeText: Showed a rapid decline in health and was treated for various periods in neonatal intensive care units. The patient also displayed severe mitral valve regurgitation with abnormal thickening of the mitral valve leaflets and pulmonary arterial hypertension. Post-mortem examination of the proband’s heart confirmed severe biatrial dilatation, significant biventricular hypertrophy with small ventricular cavities and severe mitral valve dysplasia

CaseNotHPOs: NR

CaseNotHPOFreeText: no gross developmental defects

CasePreviousTesting: No prior genetic testing reported before exome sequencing

Genotyping Method: Performed exome sequencing on the proband. Exome libraries were constructed using the Agilent SureSelectQXT Target Enrichment System for Illumina Multiplexed Sequencing Protocol (Agilent Technologies, CA). DNA libraries were captured with the Agilent Clinical Research Exome Kit. Paired-end 150 base pair reads were generated for exome-enriched libraries sequenced on the Illumina HiSeq 4000 to a targeted depth of 100× coverage

FunctionalAnalysis: Functional analysis performed. Immunohistochemical analysis of MYL2 expression in the proband’s ventricular myocardium shows a remarkable reduction in the expression of MYL2 as compared to control. Also, MYL2 mRNA was detected in the ventricle of the proband by RT-PCR. This suggests that the frameshift variant adversely affects the levels of MYL2 protein in the proband. Using immunoblot analysis, we observed that overexpression of the MYL2-fs variant was significantly reduced compared to stop-gain variants and the missense variant. When the H9c2 cells were treated with MG-132 after transfection with the MYL2-fs construct, the GFP signal corresponding to MYL2-fs was recovered. The in vitro experiments indicate that the MYL2-fs variant is not stable and that proteasome-mediated degradation of the translated product plays a key role in the instability of the protein. The overexpression of the fs variant identified in our proband or the MYL2-G162R missense variant failed to rescue the phenotype. Results reported in Figures 2, 3, and 4.

Variant: NM_000432.3:c.431_432delCT

ClinVar: NR

CAID: UnregisteredVariant

gnomAD: NR

AdditionalInfo: 4 siblings who died before 1 year of age but MYL2 genotyping was only confirmed in the proband (VI:4)

PMID: 28538763

Gene: TNNT2

HGNC ID: 11949

Case#: 11 year old girl

DiseaseAssertion: hypertrophic cardiomyopathy

FamilyInfo: unremarkable

ParentalTesting: Both parents were tested and neither carried the variant

CasePresentingHPOs: HP:0001639 HP:0011675

CaseHPOFreeText: Post-mortem examination revealed asymmetric non-obstructive hypertrophy of the interventricular septum.

CaseNotHPOs: Syncope absent

CaseNotHPOFreeText: No complaints, normal exercise tolerance, no syncope, no medications, and no significant family history.

CasePreviousTesting: Autopsy and sudden cardiac death investigation.

Genotyping Method: Genetic testing performed as part of post-mortem investigation; familial cascade screening.

FunctionalAnalysis:

Variant: TPM1 c.656A>T (p.Asp219Val, p.D219V)

ClinVar: absent

CAID: CA2998480361

gnomAD: absent

AdditionalInfo: Variant classified as likely pathogenic (Class IV) by the authors and determined to be de novo.

PMID: 27141495

Gene: TNNT2

HGNC ID: 11949

PMID: 27199119

Gene: TNNT2

HGNC ID: 11949

PMID: 29709087

Gene: MYL3

HGNC ID: 7584

PMID: 31770195

Gene: TNNT2

HGNC ID: 11949

PMID: 28669108

Gene: TNNT2

HGNC ID: 11949

Case1: Male, 37 years old, Colombian

DiseaseAssertion: asymmetric septal hypertrophic cardiomyopathy

FamilyInfo: During genetic assessment, a family history of hypertrophic cardiomyopathy (HCM) was detected. The patient’s mother had HCM and died at the age of 66; two living brothers have HCM (51 and 60 years of age). In addition, two of his brothers under the age of 35 died suddenly, two more brothers died from an unknown cause before the age of 5, and yet another brother is being examined for possible heart disease. Findings indicated a dominant inheritance pattern for HCM in this family. Pedigree shown in Figure 2.

ParentalTesting: NR

CasePresentingHPOs: HP:0001639, HP:0001663, HP:0001962, HP:000209, HP:0002315

CaseHPOFreeText: At the age of 25, his symptomatology started, including intense fatigue and mild thoracic pain due to physical activity. At the age of 32, an echocardiogram revealed asymmetric septal hypertrophic cardiomyopathy. The thickness of the interventricular septum was 19.5 mm in the basal third, 22 mm in the middle third, and 23 mm in the apical third, and ventricular tachycardia was also present. Alcohol septal ablation was performed. However, ventricular tachycardia and disabling symptoms persisted, so he required an implantable cardioverter-defibrillator at the age of 35. A routine echocardiogram at the age of 36 yielded the following findings: an LV of normal size, mild hypertrophy of the septum, normal systolic function, and diastolic dysfunction with slow LV relaxation. The patient still suffers dyspnea during physical effort and occasionally thoracic pain with palpitations

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

Genotyping Method: A molecular panel for HCM including 17 genes was performed using next-generation sequencing. Sanger sequencing chromatogram focusing on the targeted region including the variation

FunctionalAnalysis: NR

Variant: NM_000432.3:c.260G>C

ClinVar: 43461

CAID: CA009968

gnomAD: NR

AdditionalInfo: NR

PMID: 33139982

Gene: MYL2

HGNC ID: 7583

PMID: 21823217

Gene: MYL3

HGNC ID: 7584

PMID: 26498512

Gene: TNNT2

HGNC ID: 11949

Case#: Single proband ; 63-year-old female; palpitations at presentation July 2025; HCM diagnosis established at age 63

DiseaseAssertion: Hypertrophic cardiomyopathy (HCM) complicated by apical left ventricular aneurysm and mid-ventricular obstruction⁠

FamilyInfo: No family history of cardiac disease or sudden cardiac death at a young age reported. Both parents deceased (one of cancer, one of natural causes at age 92), neither with reported cardiovascular disease; proband has no siblings. Only first-degree relative is her son, who carries the KCNJ5 c.464G>A variant but not the MYBPC3 c.278delA variant, and has a normal echocardiogram with no myocardial hypertrophy. No pedigree beyond the son (Fig. 3B).⁠

ParentalTesting: Not performed; both parents deceased, no DNA available; authors state a valid familial segregation analysis could not be performed. Only one family member (son) was available for cascade Sanger screening.⁠

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy); HP:0001649 (Tachycardia), palpitations; HP:0001712 (Left ventricular hypertrophy).

CaseNotHPOFreeText: No history of hypertension, diabetes, or hyperlipidemia. Phenocopies excluded: no extra-cardiac manifestations of Fabry disease and GLA testing negative; cardiac amyloidosis excluded (no apical sparing, normal serum free light chains, negative serum protein electrophoresis and immunofixation); no significant coronary stenosis on coronary CT angiography. No QT prolongation or features of Andersen–Tawil syndrome on ECG.

CasePreviousTesting: Whole exome sequencing identified both variants; all rare and known variants validated by Sanger sequencing, with cascade Sanger screening in available one family member. No prior genetic testing reported before this episode.

Genotyping Method: Targeted region capture with next-generation high-throughput sequencing (whole exome, exonic plus flanking regions); variants confirmed by bidirectional Sanger sequencing. Cascade screening by Sanger in the son. MYBPC3 variant absent from 1000 Genomes, ESP6500, ExAC, and the Besuper local database. KCNJ5 variant absent from 1000 Genomes and ESP6500, ExAC frequency, absent from local Basenhall controls.⁠

FunctionalAnalysis: None performed; authors list absence of functional studies and lack of mRNA-level validation as limitations. MYBPC3 frameshift predicted to trigger nonsense-mediated decay.⁠

Variant: MYBPC3 NM_000256.3:c.278delA (p.Lys93ArgfsTer3); heterozygous; exon 2; novel, not in ClinVar or HGMD; classified Likely Pathogenic by ACMG (PVS1, PM2). Second variant: KCNJ5 NM_000256.3:c.464G>A (p.Arg155Gln); heterozygous; exon 2; novel, not in ClinVar or HGMD; classified VUS (PM2, PP3). Note the paper's KCNJ5 accession is written as NM_000256.3, which is the MYBPC3 transcript, most likely a typo in the article Pepper please conform for me the correct KCNJ5 accession

ClinVar: No ClinVar record for either variant; nearby KCNJ5 missense variants c.451G>A, c.452G>A, c.470T>G, and c.473C>G are documented as pathogenic/likely pathogenic for long QT syndrome or aldosteronism, and downstream frameshift/nonsense variants at the MYBPC3 locus are classified pathogenic or likely pathogenic.

CAID:Not found.

gnomAD: No allele frequency available, so no MAF to report.

PMID: 42428486

Gene: MYBPC3

HGNC: HGNC:7551

AdditionalInfo:Single-case report, no case numbering system used. Treated with dapagliflozin, metoprolol, rivaroxaban, and recombinant human BNP for 13 days, discharged on the first three; mexiletine added at 1-week follow-up for persistent palpitations. ICD recommended but declined due to financial constraints; 3-month follow-up showed good adherence with occasional palpitations and no serious arrhythmic events. Authors conclude MYBPC3 c.278delA is likely pathogenic for HCM, while the KCNJ5 variant shows no clinical phenotype in the proband or her son and may be incidental or a modifier.⁠

PMID: 27082122

Gene: TNNT2

HGNC ID: 11949

Case#: Pedigree III:2; male; HCM diagnosed clinically at age 39 (1998); heart transplant after progression to end-stage heart failure

DiseaseAssertion: Hypertrophic cardiomyopathy (HCM), progressed to end-stage heart failure with systolic dysfunction

FamilyInfo: No family history of heart disease reported at diagnosis; no known consanguinity. Parents deceased and unavailable for testing. 12 relatives genotyped: one brother (III:3) homozygous, seven first- and second-degree relatives heterozygous. All heterozygotes have normal ECG, normal echo, and no cardiac symptoms. Three children of generation IV (IV:7, IV:8, IV:9) still awaiting results.⁠

ParentalTesting: Not performed; both parents deceased. Absence of consanguinity stated but not genetically confirmed; parental phase therefore inferred rather than tested.

CasePresentingHPOs:HP:0001639 (Hypertrophic cardiomyopathy); HP:0002094 (Dyspnea); HP:0001658 (Myocardial infarction);HP:0001678 (Atrioventricular block)

CaseHPOFreeText: Exertional dyspnea at age 39 with systolic murmur; IVS 26 mm, posterior wall >16 mm, LVOT peak velocity 2.8 m/s. Pacemaker 1999, extracted 2010 for infection. 2013 circumflex occlusion treated with stent (cholesterol 6.8 mmol/L, LDL 4.6 mmol/L; former smoker). Septum 27 mm, moderate systolic dysfunction, NSVT on Holter → ICD. 2014 AF with severe dyspnea; on beta-blocker, ACE inhibitor, and aldosterone antagonist. 2016 VO₂max 14 mL/kg/min; LVEDP 24 mmHg rising to 38 with exercise, pulmonary pressure 56/27 rising to 70/… systolic. Biopsy: moderate interstitial fibrosis, focal hypertrophy and atrophy, no infiltrative disease.

CaseNotHPOs: HP:0000822 (Hypertension); HP:0000819 (Diabetes mellitus)

CaseNotHPOFreeText: BP normal throughout, no hypertension. No storage or infiltrative disease on biopsy. Spirometry normal. Narrow QRS, so CRT not indicated.

CasePreviousTesting: 84-gene cardiomyopathy NGS panel (MYBPC3 100% coverage); MLPA confirmed true homozygosity rather than hemizygous deletion; Sanger cascade in 12 relatives.

Genotyping Method: NGS panel followed by MLPA confirmation of homozygosity; Sanger for family cascade.

FunctionalAnalysis: None performed. Biopsy showed interstitial fibrosis with hypertrophy and atrophy, no infiltrative disease. Dominant-negative mechanism proposed, untested.

Variant: MYBPC3 NM_000256.3:c.2618C>A (p.Pro873His); homozygous missense; C7 domain. (Paper writes "c.2618 G>A" once, C>A is correct.)

ClinVar: Not stated; conflicting interpretations noted in the literature. Pepper please verifiy for me!

CAID: Not reported

gnomAD: AF 0.00006781 (14/206,446; 13/97,288 European non-Finnish) per the authors.

AdditionalInfo: ACMG Class 2 (likely pathogenic) heterozygous. Authors argue homozygosity drove progression to end-stage failure; alternative triggers considered, prior myocarditis (1989) and the 2013 infarct; but judged insufficient to explain severity.

PMID: 29663722 Gene: MYBPC3 HGNC: HGNC:7551

Case#: Proband(II-1)

DiseaseAssertion: DCM1Y

FamilyInfo: Chinese Han family with DCM phenotypes.

ParentalTesting: not reported

CasePresentingHPOs: HP:0001644

CaseHPOFreeText: Proband diagnosed with dilated cardiomyopathy and found to carry a TPM1 variant.

CaseNotHPOs: not reported

CaseNotHPOFreeText: not reported

CasePreviousTesting: not reported

Genotyping Method: Next-generation sequencing (NGS), confirmed by Sanger sequencing

FunctionalAnalysis: none reported

Variant: TPM1 c.340G>C (p.E114Q) missense variant

ClinVar: not found

CAID: CA392721071

gnomAD:

AdditionalInfo:

PMID: 33288880

Gene: MYL3

HGNC ID: 7584

PMID: 41999369

Gene: MYL2

HGNC ID: 7583

PMID: 31127036

Gene: MYL2

HGNC ID: 7583

Case1: Male, Infant, ethnicity not stated

DiseaseAssertion: congenital fiber-type disproportion (CFTD) and fatal infantile cardiomyopathy

FamilyInfo: The father was a healthy 20-yr old with no particular medical concerns, and there was no family history of neuromuscular or genetic disorders on either side. Both parents confirmed as heterozygous carriers of the MYL2 c.188del variant by Sanger sequencing

ParentalTesting: Both parents were confirmed as heterozygous carriers of MYL2 c.188del p.(Asn63Metfs7) by Sanger sequencing. Father confirmed as heterozygous carrier of NEB c.25435C>T p.(Gln8479)

CasePresentingHPOs: HP:0001290, HP:0001252, HP:0001640, HP:0001638, HP:0001639

CaseHPOFreeText: Newborn exam revealed normal first and second heart sound with gallop rhythm and palpable liver at the right costal margin, as well as generalized hypotonia and diminished reflexes. Echocardiogram was performed at 11 d of age and revealed patent foramen ovale with left to right shunt and right atrial enlargement. At age 5 mo, the proband was admitted to hospital in decompensated heart failure and intubated on inotropic support. Echocardiography revealed left ventricular dilatation, mild to moderate mitral valve regurgitation, and left atrial enlargement, with left ventricular function moderately to severely decreased with shortening fraction of 12% and ejection fraction of 23%. A vastus lateralis biopsy performed at 5 mo of age because of persistent muscle weakness and hypotonia revealed variability in fiber size with checkerboard pattern of 1:1 ratio of type 1 and type 2 fibers exhibiting hypotrophy of type 1 fiber size in comparison to the type 2 fibers. high lactate level (7.8 mmol/L)

CaseNotHPOs: NR

CaseNotHPOFreeText: Gomori trichrome–stained light micrographs and electron microscopy (EM) showed no evidence of ragged red fiber or nemaline rods, and oxidative stains revealed no evidence of cores, targetoid, or target fibers. Normal serum creatine kinase level. Normal birth weight, length, and head circumference. There was no histopathologic evidence of Pompe disease and GAA enzyme-level testing was normal. Genetic testing for POLG and Noonan syndrome genes normal

CasePreviousTesting: Genetic testing was performed for DNA polymerase γ, catalytic subunit (POLG) and Noonan syndrome genes (PTPN11, SOS1, KRAS, RAF1, BRAF, MAP2K1, MAP2K2, and HRAS), all of which were normal. There was no histopathologic evidence of Pompe disease and GAA enzyme-level testing was normal. Muscular dystrophy was considered unlikely given the histopathologic findings and normal serum creatine kinase level.

Genotyping Method: Next-generation sequencing was performed by the Laboratory for Molecular Medicine (LMM) of Partners Healthcare Personalized Medicine using the Agilent SureSelect Design process. The gene panel utilized an all exon approach for 43 genes of interest for neuromuscular and cardiac conditions by targeting coding exons with bait out to coding sequence (CDS) ±65 bases. The complete coding regions of all genes were sequenced to average depth of 316 reads

FunctionalAnalysis: No functional analysis of the variant was performed

Variant: NM_000432.3:c.188del

ClinVar: NR

CAID: UnregisteredVariant

gnomAD: NR

AdditionalInfo: This case also has a heterozygous pathogenic NEB variant c.25435C>T p.(Gln8479*) inherited from the father, classified as pathogenic but considered unlikely to be a significant contributor to disease as no second NEB allele was identified.

PMID:30565988

Gene:TNNT2

HGNC ID:11949

PMID:41969674

Gene:TNNT2

HGNC ID:11949

PMID:39905734

Gene:TNNT2

HGNC ID:11949

PMID:20973921

Gene:TNNT2

HGNC ID:11949

PMID : 40008267

Gene: TNNT2

HGNC ID: 11949

PMID: 37646638

Gene: TNNI3

HGNC ID: 11947

PMID:22957257

Gene:MYL3

HGNC ID:7582

PMID: 19087273

Gene: TNNT2

HGNC ID: 11849

PMID:38548731

Gene:TNNI3

HGNC ID:11947

PMID:28382084

Gene:TNNI3

HGNC ID:11947

PMID:30953456

Gene:TNNI3

HGNC ID:11947

PMID:40656892

Gene:TNNI3

HGNC ID:11947

PMID:33777698

Gene:TNNI3

HGNC ID:11947

PMID:28223422

Gene:MYL2

HGNC ID:7583

PMID: 18651846

Gene: TNNT2

HGNC ID: 11949

PMID: 19293840

Gene: MYH7

HGNC ID: 7577

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

A novel ACTC1 mutation in a young boy with left ventricular noncompaction and arrhythmias

PMID: 28491642

Gene:ACTC1

HGNC ID:143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID:28491642

Gene:ACTC1

HGNC ID:143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

CasePresentingHPOs: HP:0004756

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

A novel ACTC1 mutation in a young boy with left ventricular noncompaction and arrhythmias PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID:28491642

Gene:ACTC1

HGNC ID:143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID 143

A novel ACTC1 mutation in a young boy with left ventricular noncompaction and arrhythmias PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 41550885 Gene: MYBPC3 HGNC: 7551

PMID: 42460955

Gene: MYBPC3

HGNC ID: 7551

PMID: 27082122

Gene: MYH7

HGNC ID: 7577

Gene: PRKAG2

HGNC ID: 9386

PMID: 42074559

Gene: MYL2

HGNC ID: 7583

PMID: 36945405

Gene: ACTC1

HGNC ID: 143

PMID: 40298995

Gene: VWF

HGNCID: HGNC:12726

PMID: 36128439

Gene: MYL2

HGNC ID: 7583

PMID: 24992688

Gene: TNNT2

HGNC ID: 11949

PMID: 21823217

Gene: MYL2

HGNC ID: 7583

PMID: 27238910

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

PMID: 40673043

Gene: VWF

HGNCID: HGNC:12726

PMID: 37271167

Gene: MYBPC3

HGNC ID: 7551

PMID: 23494605

Gene: TNNT2

HGNC ID: 11949

PMID: 24020726

Gene: ABCA4

HGNC ID: 34

PMID: 24444108

Gene: ABCA4

HGNC ID: 34

Comment by Janneke_Adema: Is this true within an academic publishing context? First copy costs remain substantially high: editing, review, typesetting, server and band with costs, marketing etc. are still part of a digital only model. One thing that is important to explore though is what these first copy costs consist off in a digital context, to explore from there what the profit margin is that publishers put on top (plus cost for printing etc.). This could lead to the development of perhaps a more fair and transparent system based on actual costs. For books the OAPEN-NL project tried to do exactly this: https://openreflections.files.wordpress.com/2011/03/oapen-nl-final-report.pdf

https://web.archive.org/web/20260207172030/https://firstmonday.org/ojs/index.php/fm/announcement/view/99

First Monday, open internet journal will cease publication in May 2026.

Nature Medicine "A minimally invasive dried blood spot biomarker test for the detection of Alzheimer's disease pathology" Jan 5, 2026. The abstract does not mention the 10-20yr early warning finding.

This is the actual link https://www.nature.com/articles/s41591-025-04080-0

Added A minimally invasive dried blood spot biomarker test for the detection of Alzheimer’s disease pathology in Zotero

This quote highlights the important ethical dimension of digital archaeology. Showing how open access and collaborative tools in digital archaeology challenge corporate control over knowledge. It aligns with using open GIS platforms that I will use for my projects and open data policy.

PMID: 37288251

Gene: SCN5A

HGNC ID: 10593

PMID: 38638373

Gene: NR

HGNC ID: NR

PMID: 40364801

Gene: SERPING1

HGNC ID: 1228

Is this true within an academic publishing context? First copy costs remain substantially high: editing, review, typesetting, server and band with costs, marketing etc. are still part of a digital only model. One thing that is important to explore though is what these first copy costs consist off in a digital context, to explore from there what the profit margin is that publishers put on top (plus cost for printing etc.). This could lead to the development of perhaps a more fair and transparent system based on actual costs. For books the OAPEN-NL project tried to do exactly this: https://openreflections.files.wordpress.com/2011/03/oapen-nl-final-report.pdf

Not that it would've helped in this instance, but a reminder of https://libguides.uky.edu/OpenAccess/discounts

A systemic problem where the current publishing structure has the wrong incentives for authors, publishers, and others. If we are to solve the access problem (with some flavor of open access), how can the incentives be changed to account for this bad research problem? Are changes to finding models a net positive or negative effect on the trustable nature of the published research?

The most prominent example of this type of online curation, in my personal experience as a teacher, is curating reading lists for my university courses.

In some cases (more "traditional"), this list is part of the syllabus and coursepack that I distribute ahead of the semester so it's something that I would do in the Summer or during a Winter break. Having taught several courses on a short notice (getting the contract a couple of weeks before the semester starts), I've fine-tuned my technique to be as efficient as possible. Some of my reading lists were better than others and a few were really solid. Teaching with such a reading list is quite a joy. Much more so than teaching from a textbook. At one point, I stopped having printed coursepacks. I simply give links to the fulltext articles available through #OpenAccess or through the databases to which the university's library is subscribed. A few students complained early on but it does mean that they don't have to purchase text material for the course. The reason it's important to me does have to do with the cost of higher education. It's also about shifting the role of text resources. We use these texts to do some work together. It's not like these texts are "transmitting the knowledge" to learners' brains.

So, that's my more traditional pattern: a syllabus with a list of links to articles (typically PDFs) that I distributed before the semester starts.

In other cases (my "enhanced" practice), it's something I do every week, based on what has happened in the course. And I do mean a full reading list each week. Class members choose the text on which they want to focus. Though several of them expect me to be "the sage on the stage" who will lead them to that one nugget of wisdom they will have to "retain", a shift happens once they take ownership of those reading choices. That practice is quite timeconsuming and it doesn't necessarily improves my teaching in obvious ways. It's rewarding in other ways. (I sometimes ask learners to find resources on their own, which really deepens the learning process. It requires a significant level of autonomy that they might not reveal during a given semester, even if they have significant experience as university students).

My routine of building weekly reading lists also means that I got quite a bit of practice at this.

Typically, I start the collecting with a "forward citation search" in Web of Knowledge, Scopus, or Google Scholar. I often know this one key article which is likely to have been cited by a number of authors more recently. I collect as many of those as possible and some patterns emerge. Quite frequently, there would be subtopics that I rearrange. It might send me in a "rabbithole". Which is ok. I'm in a discovery mode. And some of the texts which fall under my radar at that point become relevant at a further point.

In other words, I often cast a wide net during the collection phase.

The selection process is mostly a matter or rearranging the reading list so that the first few items cover enough of the range of subtopics. Sometimes, my lists remain quite long, which means that learners have more choice (which is uncomfortable enough to help them learn). It also involves an organization phase.

Summarizing the significance of the collection is the basis for my presentation of the list to the class. My description of the collection is the moment in a class meeting during which I switch to lecture mode. If I do it at the end of the class meeting (or just before the break), students are likely to pay less attention, even though it's typically short. If I do If I do it before discussing the items for the current week, it gets a bit confusing. So it often works best if I present this list after we've worked through the previous ones but before some kind of activity which links the two topics.

As for sharing in the cloud, I typically do this through the LMS I'm using in that institutions. I've tried more public methods but they weren't that effective.

All this to say... I could probably optimize my method.

You can keep up on overall open access news from the University of California system online.

A summary of Plan S, the European plan to support open access publishing.

FAQs on open access policies from the Open Research Funders Group.

Openaccess parable.

list of open access publishing tools

Is this true within an academic publishing context? First copy costs remain substantially high: editing, review, typesetting, server and band with costs, marketing etc. are still part of a digital only model. One thing that is important to explore though is what these first copy costs consist off in a digital context, to explore from there what the profit margin is that publishers put on top (plus cost for printing etc.). This could lead to the development of perhaps a more fair and transparent system based on actual costs. For books the OAPEN-NL project tried to do exactly this: https://openreflections.files.wordpress.com/2011/03/oapen-nl-final-report.pdf

This doesn't sound like a problem to me. Individual research communities should be able to adopt an OA style that works for them. I've never thought it realistic that the sciences and humanities will pick the same kind of OA, it's never been clear to me why it even needs to be the same kind, but [deity] do we waste a lot of breath and text talking about this.

OA can be paired with OER

My paper is actually open access at the original journal site, here: https://asis.org/Bulletin/Apr-13/AprMay13_Mounce.html

Please don't pay to access it from here!

I had no idea Wiley had any arrangement with ASIST to sell access to my article. It's pretty unethical to sell access to an authors work without their consent if you ask me!