Achieving low-cost sequencing requires high-throughput scale, and most genomics companies cannot reach it alone. In the LSMC foundry your samples run in a fully scaled lab, with the cost and consistency of a mature production line.
Observed NIST GIAB HG002 read evidenceNIST GIAB HG002 · GRCh38Coverage and observed reads load across the window, resolve a benchmark event, and cycle through an SNV, insertion, deletion, structural deletion, and tandem duplication. BRAF SNV at chr7:140,752,937. 60 of 139 informative reads support the benchmark event.
HG002GRCh38chr7:140,752,93760 / 139 reads
A genome foundry is a scaled lab that generates data to spec.
We help a team decide which genome product to make, what variant classes it needs to support, what quality standard it has to meet, and what deliverable comes back at the end.
The genome products
Four genomes, built on one line.
From imputed low-pass at population scale to a full short-read and long-read hybrid, LSMC manufactures four genome products against the same quality gate. Choose by the resolution the program needs.
High Resolution Hybrid Genome$$$$
Industry Standard Genome$$$
Cost Optimized Genome$$
Low-Pass Genome$
Production workflow
See how a sample moves through the genome manufacturing workflow and becomes a finished genome data product.
StageWhat it controls
Define the needapplication · scope
Choose a genome productlow-pass to hybrid long-read
Set variant classesSNV · indel · SV/CNV · pharmacogenomics
Define the intended useresearch or clinical
Run productionacceptance gates · contamination
Return the dataturnaround SLA · VCF/BAM/CRAM
Infrastructure, not service provider.
We become your production team, giving you a CLIA-certified lab, the flexibility of a contract sequencing provider, and the speed and cost of a scaled facility.
Inside LSMC
How LSMC works, end to end.
CLIA-certified
South San Francisco
Four genome products
From specification to finished data.
See how LSMC connects program design, genome production, and data delivery in one manufacturing system. A program starts as a specification, and the foundry returns it as finished genome data.
Genome program planner
Match your program to the right genome product.
Start from the application or from the resolution you already want. The planner translates that choice into product fit, scope gaps, turnaround, and indicative program economics.
Clinical-readyResolved to clinical grade, callable and reportable.
Research-gradeUsable for discovery; not for clinical reporting as-is.
ImputedInferred from low-pass. This is broad signal, not direct observation.
Higher productAvailable by moving up to a higher genome product.
Not supportedA different product in the line covers this class.
Grades are a projection of platform capability per class. They are firmed up against audited production data as each line comes online.
The genome products
The four genome products.
How the Industry Standard Genome compares.
Select an axis to read its definition.
Axis scores are a normalized 0–100 read of platform capability. They are directional and provided for orientation, not as a guarantee. The performance contract below sets the figures LSMC holds each run to.
Axis
Low-Pass
Cost Opt
Industry Stdselected
High-Res Hybrid
47
78
85
96
70
92
94
97
45
75
88
96
–
18
35
92
20
30
45
92
The performance contract
What the Industry Standard Genome guarantees.
Every run is held to these acceptance criteria at the quality gate. If it does not meet them, it does not ship.
SNV sensitivity / precisiongenome-wide
≥ 99.8%
Indel F1≤50bp
≥ 99.5%
SV sensitivitylarge events
≥ 90%
Callabilityfull-depth WGS
≥ 98%
Contaminationacceptance gate
< 1.0%
Turnaround SLAstandard turnaround
14–18 days
Indicative performance characteristics, projected from validated platform capability. Final figures are firmed up per program against audited production data.
What each product is for
1–4× · imputed
Run at 1–4× depth, the Low-Pass Genome trades per-base certainty for breadth, then imputes common variants from large reference panels. It resolves broad common-variant signal and polygenic scores across populations; common indels are imputed alongside SNVs, while structural variants and anything needing direct full-depth observation are out of scope. It is the lowest-cost path LSMC manufactures.
$
Cost-optimized short-read · SNVs and indels at clinical grade
A short-read genome tuned for cost. SNVs and small indels are called at clinical grade; copy-number and structural variants come at research grade, not clinical. Full depth, for programs that do not need maximum structural resolution.
The LSMC short-read baseline genome, run at full depth on the validated caller stack. It calls SNVs and small indels at clinical grade and resolves most structural variants. The standard genome for programs that need reliable, whole-genome short-read coverage without the long-read arm.
Two sequencing methods in one assay. The short-read arm delivers high base-level accuracy across the whole genome, calling SNVs and small indels, while the long-read arm resolves what short reads cannot: structural variants, repeat expansions, and segmental duplications, and phases the result. The widest-reaching genome LSMC manufactures, clinical-ready across every class.
$$$$
From sample to finished genome data
About LSMC
LSMC is the infrastructure genomic innovators build on.
Genomics can transform science and medicine, but only if the data that drives innovation can scale. Too much effort today goes into rebuilding the same sequencing operations. LSMC runs that operation once, so its customers do not have to build it again.
Proven operators
The operators behind the foundry.
The founding team combines genomics product strategy, high-throughput laboratory operations, automation, bioinformatics, and experience scaling clinical sequencing systems.
CEO
Eric Olivares, Ph.D.
Eric is known for helping companies make high-conviction bets while avoiding the landmines that derail the move from R&D to commercialization. He has led product, technology, and scientific strategy through growth, scale, and reinvention, aligning scientific rigor with commercial execution.
Invitae
GeneDx
Variantyx
PacBio
Informatics
John Major
For over twenty years, John has worked at the forefront of genomics, from contributing to the Human Genome Project to scaling leading genetic-testing companies. He was a leader at Invitae as it grew from a small lab to more than two million samples per year, with deep experience in high-throughput sequencing, bioinformatics, and process automation.
Human Genome Project
Invitae
Automation
John Whittaker
John has led the design and operation of large-scale clinical genomics laboratories at Labcorp and Invitae. He built hardware, software, and automation systems for one of the world’s largest clinical sequencing operations, where reliability and reproducibility are essential.
Labcorp
Invitae
Work with LSMC.
Contact
Tell us what you’re trying to run.
LSMC reviews each inquiry and responds with a proposed program scope and an indicative price.
