ivelsko (velsko@shh.mpg.de)
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Sterling Wright (sterlingwright2016@utexas.edu)
2021-03-02 21:30:24

Do people have a particular vendor or software that they like (or absolutely hate) for organizing their lab purchases, funding allocations, inventory, etc? We are considering spendlab or quartzy but open to other suggestions

Giada Ferrari (gferrari.rbge@gmail.com)
2022-06-01 12:08:35

Hi 🙂 Has anyone replaced AMPure XP beads with NEBNext sample purification beads for library clean up, and if so, did you stick to the bead to library ratio from the original protocol?

irinavelsko (irinavelsko@gmail.com)
2023-05-08 11:25:26

Hi All, at SPAAM2 we discussed testing consistencies and biases across labs with a shared sample extraction/sequencing project. Here's an example of one such project on modern DNA https://www.biorxiv.org/content/10.1101/2023.04.28.538741v3

bioRxiv
Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols
Background Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5x human stool samples and 2x mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. Results A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. Conclusion This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.04.28.538741v3
👍 Sterling Wright
👍:skin_tone_6: Miriam Bravo
irinavelsko (irinavelsko@gmail.com)
2023-09-18 11:16:51

Hi @channel to follow up on the short discussion we had a SPAAM5 last week, I'd like to bring up the idea of a pan-lab extraction and library build project to identify differences between the sequencing results when starting with the same sample material

irinavelsko (irinavelsko@gmail.com)
2023-09-18 11:18:03

Maybe we can start by getting an idea of who is interested or might be interested. Who would be interested in participating in a project like this?

🙋‍♂️ Marcel Keller, Gunnar Neumann, Biancamaria Bonucci, Sterling Wright, Jamie Wood
🙋‍♀️:skin_tone_2: Kelly Blevins
🙋‍♀️ Ele, Oya Inanli, Elena Zavala, Sierra Blunt
Maria Lopopolo (maria.lopopolo1989@gmail.com)
2023-09-18 11:39:18

*Thread Reply:* Will it involve lab work? I ask bc we do not have one of our own for my group.

irinavelsko (irinavelsko@gmail.com)
2023-09-18 12:15:53

*Thread Reply:* Yes, it will be extracting and building a library from a sample that gets sent to all participating labs

irinavelsko (irinavelsko@gmail.com)
2023-09-18 12:16:07

*Thread Reply:* Do you share an ancient lab with another group that would be interested in participating?

Maria Lopopolo (maria.lopopolo1989@gmail.com)
2023-09-18 12:28:40

*Thread Reply:* would be @Biancamaria Bonucci

Biancamaria Bonucci (biancamaria.bonucci@ut.ee)
2023-09-18 12:41:51

*Thread Reply:* Yes!! Thank you so much! I was speaking with James and other people already about this and I would be really glad to participate and divide the work!!

🙌 Maria Lopopolo
Sterling Wright (sterlingwright2016@utexas.edu)
2023-09-19 21:51:25

*Thread Reply:* We at Penn State will be interested in joining if you are still looking for labs.