Weekly Reading List: June 16, 2025

We believe the best hope for saving science and, perhaps, saving our form of democracy, is convincing at least a couple dozen Republican members of Congress that it’s up to them—that the stakes require exercising the prerogatives of the Congress to constrain excesses by the Executive Branch and resuming the serious conversations, debates, and compromise across the aisle and between the branches that used to be the way policy was made.

Several hundred NIH employees signed on to a letter rebuking agency actions since the start of President Trump’s second term

Inversions are a unique type of balanced structural variants (SVs) with important consequences in multiple organisms. However, despite considerable effort, this and other complex SVs remain poorly characterized due to the presence of large repeats. New techniques are finally allowing us to identify the full spectrum of human inversions, but the number of individuals analyzed is still quite limited. Here, we take advantage of Oxford Nanopore Technologies (ONT) long reads to characterize an exhaustive catalogue of 612 candidate inversions between 197 bp and 4.4 Mb of length and flanked by <190-kb long inverted repeats (IRs). For that, we developed a bioinformatic package to identify inversion alleles reliably from long read data. Next, using a combination of different DNA extraction, library preparation, and ONT sequencing protocols, we showed that ultra-long reads (50-100 kb) and adaptive sampling are an efficient method to detect most human inversions. Lastly, by analyzing ONT data from 54 diverse individuals, 87-99% of the inversions could be genotyped in each sample, depending mainly on read and IR length and genome coverage. Both orientations were observed for 155 of the analyzed regions (frequency 0.01-0.49), which multiplies by three the polymorphic IR-mediated inversions studied in detail so far. Moreover, we found more than 300 additional independent SVs in the studied regions and resolved several complex rearrangements. Our work therefore provides an accurate benchmark of those inversions that typically escape most analyses, improving existing resources, such as the Pangenome. In addition, it demonstrates the potential of nanopore sequencing to determine the functional impact of missing human genomic variation.

The detection of circulating tumor DNA (ctDNA) after curative-intent therapy, referred to as molecular/minimal residual disease (MRD), is prognostic of disease recurrence in early-stage breast cancer (EBC). Tumor-agnostic approaches that rely on mutation-based assessment in fixed panels of common cancer driver genes have shown limited utility for detecting MRD in EBC. Methylation-based MRD (mMRD) may overcome the limitations of genomic-based MRD (gMRD), though limited clinical validation is available.

Simulated lab accidents train students how to respond to real emergencies.

A lawsuit filed by 27 states and the District of Columbia seeks to stop 23andMe from selling its consumer genetic data without the express consent of each customer in the company's database.

Developed by former MIT researchers, focused research organizations (FROs) undertake large research efforts and have begun to contribute to scientific advances.

Here’s a breakdown of what we know about the eight new members of the CDC’s vaccine advisory panel selected by health secretary Robert F. Kennedy Jr.

This week's American Society for Mass Spectrometry annual meeting in Baltimore saw a number of new instrument releases with vendors introducing new versions of popular proteomics-focused platforms as well as systems aimed at building out their biopharma and multiomics portfolios.

Researchers urged the NIH Director to restore grants delayed or terminated for political reasons so that life-saving science can continue.

Agency calls research to identify viral threats “unsafe”

Companies selling authorship slots thrive in a culture that equates success with a strong publication record. Customers, sleuths and the shadowy owner of a paper mill explain why.

During a Senate hearing, National Institutes of Health (NIH) Director Jayanta Bhattacharya, M.D., Ph.D., said the last few months have been “bumpy,” while underscoring Congress’ role in approving a | During a Senate hearing, National Institutes of Health Director Jayanta Bhattacharya, M.D., Ph.D., described the past few months as “bumpy,” while underscoring Congress’ role in approving a budget and taking full responsibility for the agency’s move away from “politicized science.”

Kári Stefánsson, who last month left the Icelandic genetics company deCODE, spoke to Nature about his legacy.

“Our nation’s top health official cannot be trusted to protect America’s children and their families,” writes Richard Besser, pediatrician and president of the Robert Wood Johnson Foundation.

Scientist accused months ago of shipping material, described as related to worms, to University of Michigan lab

But turning what they find into drugs isn’t so easy

Rapid uptake of big data and technologies in healthcare are transforming methodological capabilities in medicine and public health, giving rise to new fields such as precision public health. We conceptualised precision public health as an emerging technology to understand the emergence of this term and its associated characteristics.

Antibiotic development has declined in recent decades. Now, after 50 years, a new antibiotic has been created to tackle bacterial infections.

Developmental disabilities and congenital anomalies are common pediatric conditions that often require extensive genetic testing to determine an underlying cause. Traditionally, chromosomal microarrays (CMA) and Fragile X testing have served as first-tier diagnostics, but these tests are limited in scope and often necessitate follow-up sequencing assays. Whole Genome Sequencing (WGS) offers a single, comprehensive assay capable of detecting a broad spectrum of genetic variation, including single nucleotide variants (SNVs), insertions and deletions (INDELs), copy number variants (CNVs), structural variants (SVs), loss of heterozygosity (LOH), and tandem repeat alterations. In this study, we evaluated whether WGS could replace CMA and serve as a more effective first-tier test. WGS achieved a 97.28% concordance with CMA for clinically relevant CNVs and LOH, while also offering more accurate breakpoint resolution and broader data point coverage. Notably, 4 out of 5 discordant cases (80%) were due to WGS providing more accurate breakpoint resolution. WGS covered over 97% of clinically relevant regions for CNV detection, compared to < 3% with CMA. To address the interpretive burden associated with the increased CNV calls, we implemented a cohort-based occurrence filter that successfully prioritized potential pathogenic events without sacrificing clinical sensitivity. Additionally, we assessed the feasibility of Fragile X screening from WGS data using a custom PCR confirmation logic built on Expansion Hunter output. This approach accurately excluded normal-range alleles and flagged indeterminate or expanded alleles for follow-up PCR confirmation. Our results support the use of WGS as a scalable and comprehensive diagnostic platform capable of consolidating multiple traditional assays. By streamlining workflows and enhancing clinical resolution, WGS offers a compelling alternative to the current diagnostic paradigm for patients with suspected genetic disorders. ### Competing Interest Statement N.L. received personal fees from Illumina Inc and is a scientific advisory board member for FYR Diagnostics, ML4H, and Everygene, Inc. V.P. is a former employee and owns shares of Illumina. ### Funding Statement This study was funded by Quest Diagnostics and Broad Clinical Labs ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Institutional Review Board of WCG gave ethical approval for this work (IRB protocol identifier 20242498). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.

Thermo Fisher Scientific said Thursday that the Regeneron Genetics Center (RGC) has launched a large-scale proteomics research project involving nearly 200,000 patient samples from the Geisinger Health Study and has chosen the Olink Explore HT proteomics platform for the effort.

Anne Wojcicki to buy back 23andMe and its data for $305 million

Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally challenging to obtain and are thus often unavailable for samples without established cell lines. Here, we introduce hifiasm (ONT), the first algorithm that can produce near T2T assemblies from standard ONT Simplex reads, eliminating the need for ultra-long sequencing. Compared to existing methods, hifiasm (ONT) reduces the computational demands by an order of magnitude and reconstructs more chromosomes from telomere to telomere on the same datasets. This advancement substantially broadens the feasibility of T2T assembly for applications previously limited by the high cost and experimental requirement of ultra-long reads. ### Competing Interest Statement Sean McKenzie, Katherine R. Lawrence, Rhydian Windsor, and Mike Vella are employees of Oxford Nanopore Technologies. The remaining authors declare no competing interests.

For Illumina, its former employees are both a boon and a problem. In the 27 years since its founding, the DNA sequencing company unlocked new frontiers in biology, medicine and…

District judge could declare terminations unlawful—or toss suit based on technicalities