Genomics

Metagenomic diagnosis and pathogenic network profile of SARS-CoV-2 in patients co-morbidly affected by type 2 diabetes

1. Hassan M. Al-Emran
2. M. Shaminur Rahman
3. Md. Shazid Hasan
4. A. S. M. Rubayet Ul Alam
5. Ovinu Kibria Islam
6. Ajwad Anwar
7. Iqbal Kabir Jahid
8. M. Anwar Hossain

Reviewed by ScreenIT

Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates

1. Ahmed M Moustafa
2. Colleen Bianco
3. Lidiya Denu
4. Azad Ahmed
5. Susan E Coffin
6. Brandy Neide
7. John Everett
8. Shantan Reddy
9. Emilie Rabut
10. Jasmine Deseignora
11. Michael D Feldman
12. Kyle G Rodino
13. Frederic Bushman
14. Rebecca M Harris
15. Josh Chang Mell
16. Paul J Planet

Reviewed by ScreenIT

Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes

1. Melissa Bothe
2. René Buschow
3. Sebastiaan H Meijsing

Reviewed by Review Commons

High social status males experience accelerated epigenetic aging in wild baboons

1. Jordan A Anderson
2. Rachel A Johnston
3. Amanda J Lea
4. Fernando A Campos
5. Tawni N Voyles
6. Mercy Y Akinyi
7. Susan C Alberts
8. Elizabeth A Archie
9. Jenny Tung

• Curated by eLife

  Evaluation Summary:

  In this paper, the authors collect epigenomic data from a well-studied wild baboon community, which they use to construct an epigenetic clock, a method of measuring "biological age" that is increasingly used as a tool in human aging research. The authors find that deviations between biological and chronological age can in part be explained by social phenomena. In particular, for male baboons, maintaining social dominance may play an important role in accelerating the dimension of aging indexed by this measure. This is a foundational study for social-biological-health research.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

1. Bas B. Oude Munnink
2. Reina S. Sikkema
3. David F. Nieuwenhuijse
4. Robert Jan Molenaar
5. Emmanuelle Munger
6. Richard Molenkamp
7. Arco van der Spek
8. Paulien Tolsma
9. Ariene Rietveld
10. Miranda Brouwer
11. Noortje Bouwmeester-Vincken
12. Frank Harders
13. Renate Hakze-van der Honing
14. Marjolein C. A. Wegdam-Blans
15. Ruth J. Bouwstra
16. Corine GeurtsvanKessel
17. Annemiek A. van der Eijk
18. Francisca C. Velkers
19. Lidwien A. M. Smit
20. Arjan Stegeman
21. Wim H. M. van der Poel
22. Marion P. G. Koopmans

Reviewed by ScreenIT, NCRC

Evolution of cytokine production capacity in ancient and modern European populations

1. Jorge Domínguez-Andrés
2. Yunus Kuijpers
3. Olivier B Bakker
4. Martin Jaeger
5. Cheng-Jian Xu
6. Jos WM Van der Meer
7. Mattias Jakobsson
8. Jaume Bertranpetit
9. Leo AB Joosten
10. Yang Li
11. Mihai G Netea

• Curated by eLife

  Evaluation Summary:

  Dominguez-Andrés et al. collect a large amount of immune-related trait association data from a cohort made up of 534 individuals of Western European ancestry. The goal was to track the evolutionary trajectories of cytokine production capacity over time in a number of patients with different exposure to infectious organisms, infectious disease, autoimmune and inflammatory diseases, using the 500 Functional Genomics cohort of the Human Functional Genomics Project. From this analysis it was hypothesized that the Neolithic transition was characterized by strong changes in the adaptive response to pathogens in human biology. Overall, the manuscript is interesting but could be improved by significant enhancements to statistical methodology.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Improving oligo-conjugated antibody signal in multimodal single-cell analysis

1. Terkild B Buus
2. Alberto Herrera
3. Ellie Ivanova
4. Eleni Mimitou
5. Anthony Cheng
6. Ramin S Herati
7. Thales Papagiannakopoulos
8. Peter Smibert
9. Niels Odum
10. Sergei B Koralov

Reviewed by eLife

In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

1. Juan Carlos Jado
2. Michelle Dow
3. Krypton Carolino
4. Adam Klie
5. Gregory J. Fonseca
6. Trey Ideker
7. Hannah Carter
8. Elizabeth A. Winzeler

• Curated by eLife

  Summary: The authors examined the genomic basis of resistance evolution in human chronic myelogenous leukemia (CML) near-haploid cell lines to 5 separate chemotherapeutic agents.

  Using either whole genome or whole exome analysis, they found numerous instances of single nucleotide polymorphisms and copy number variants, including amplifications and deletions, among lines. They then used subsequent knockdown or knockout experiments to confirm that these variants, in fact, lead to increased resistance in these lines.

  The work is interesting, timely, and has potential clinical implications. For example, the resistance alleles identified here could be closely examined in future studies in order to develop treatment strategies. However, the experimental design has certain limitations, advances in understanding chemotherapy resistance mechanisms is currently modest, and the presentation of results can be improved. We feel overall that these could be addressed, but that they will require significant extra experimental work.

Reviewed by eLife

Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

1. Andrew D Skol
2. Segun C Jung
3. Ana Marija Sokovic
4. Siquan Chen
5. Sarah Fazal
6. Olukayode Sosina
7. Poulami P Borkar
8. Amy Lin
9. Maria Sverdlov
10. Dingcai Cao
11. Anand Swaroop
12. Ionut Bebu
13. DCCT/EDIC Study group
14. Barbara E Stranger
15. Michael A Grassi

Reviewed by eLife

Gene expression variability in human and chimpanzee populations share common determinants

1. Benjamin Jung Fair
2. Lauren E Blake
3. Abhishek Sarkar
4. Bryan J Pavlovic
5. Claudia Cuevas
6. Yoav Gilad

Reviewed by eLife