myBaits® Custom Target Capture Kits

myBaits® custom kits provide focused NGS hybridization capture panels for any organism and any project size.

Custom kits provide in-solution biotinylated RNA probes complementary to sequences of interest, which allow rapid, selective target enrichment for highly cost-effective next-generation sequencing (NGS).

In-solution probes allow for specific, yet flexible hybridization to complementary target molecules, which provides the ability to recover variable regions from taxonomically divergent species and strains. This allows capture probes to be successfully employed even on non-model organisms which lack a sequenced genome or transcriptome. myBaits kits have been successfully used in research projects from hundreds of genome types including animals, plants, and microbes and from fresh, degraded, and environmental DNA sources.

myBaits custom sequence capture kits utilization across a wide variety of organisms and applications make them the perfect choice for any targeted NGS project. Arbor Biosciences’ proprietary oligo synthesis platform allows flexible production of high-quality baitsets at extremely competitive pricing for any project size. The kits are perfect for new or expert users as the easy to follow protocol delivers consistently reproducible results. Our team of expert scientists will assist with a streamlined complimentary bait design process and provide experimental design advice as needed in order to deliver a successful project. If a complete solution is needed, from sample preparation to data delivery, our myReads services team is available to handle projects of any size.

Features & Benefits

Affordable and scaleable
Kit sizes available for any size project
Easy design
Design your probes from any nucleic acid source -- genomes, transcripts, SNPs, etc
Scientific expertise
Free bait and project design assistance from our team of expert scientists
Convenient kits
Each order includes probes and hybridization/washing reagents

Figure 1. How does myBaits work? (1) HYBRIDIZATION – An NGS library is denatured via heat, and allowed to hybridize to a complex mixture of complementary biotinylated RNA baits over the course of several hours. Adapter-specific blocking oligos prevent random annealing of library molecules at the common adapter sites. (2) WASHING – After the hybridization is complete, the biotin present on each bait is bound to a streptavidin-coated magnetic bead. Wash steps help remove off-target or poorly-hybridized library molecules. (3) AMPLIFY – The remaining library molecules that are still bound to their complementary baits are denatured via heat, and amplified using universal library primers. This “enriched” library can now be sequenced.


Figure 2. Typical example visualizing NGS reads from enriched human gDNA library, aligned to the hg38 genomic reference sequence. Positions of the four 80nt myBaits probes in this region are indicated by blue bars. Unique read coverage is highest across the baited region, and tapers off upstream and downstream of the baited region. If sequencing further into the known or unknown flanking regions is desired, simply increase the length of your NGS library molecules (compatible with any myBaits kit).

We are pleased to provide as much bait design advice and assistance as possible. However we are unlikely to be sufficiently knowledgeable in your particular field as to help you pick the specific genes/targets for your project. Whether this is your first NGS project and/or you are an experienced genetics researcher, we always recommend that you choose your targets in collaboration with your full research team, especially your bioinformatician(s), so that your kit design is as robust as possible.

Some general suggestions appropriate for many projects would be to exhaustively survey the literature for your organism(s), and consider including neutral and/or control loci in addition to specific targets of interest. You should include enough loci and/or SNPs to draw significant conclusions within the number of specimens that you plan to survey. You should make sure that you have thoroughly evaluated your bait design before proceeding with your kit order.

If you are beginning a completely new project, you may wish to order the smallest number of reactions upfront, and place a re-order for a larger number of reactions once you have tested the design. However just note that any changes (add/drop baits) to your design would need to be manufactured as a new custom kit, which has longer delivery times than a reorder of a previous design.

myBaits Submission Guidelines

Please gather your target sequences in FASTA format or as genomic coordinates according to our guidelines, and contact us with the details of your project to obtain a Quote. Please let us know upfront if there is a specific kit size in which your design should be constrained (e.g. a myBaits-3 kit with up to 60,000 probes) so that together we can adjust your bait design accordingly. Otherwise, we can let you know the estimated price of your design after processing your sequences.

The bait manufacture turnaround time varies depending on the specific baitset and the number of other kits in our queue, but it is typically ~8 weeks minimum for your baits to pass our QC process. Our turnaround time is necessary so that we can carefully manufacture your custom probes according to our high-quality standards. Please do NOT wait until the last minute to place your order, as we cannot rush orders. We are continually working to reduce manufacturing turnaround times.

Also, please consider that if you choose to utilize our complementary bait design services, we will typically be in correspondence for an additional upfront period (up to several weeks) regarding a design before we can proceed to the bait manufacturing (see above). This can be skipped if you provide us with pre-designed probes that do not require any additional design work. Please remember to accommodate additional time for your collaborators to approve the final design.

Capturing individual libraries produces the best per-sample results. However, multiple dual-indexed libraries can be pooled into single capture reactions (e.g. “multiplexing”) in order to assay more samples with a smaller kit. For new baitsets, we strongly recommend first performing trial captures with different pooling schemes to determine what works best for your particular samples and bait set. When pooling libraries that vary in relative target content (e.g., ancient, forensic, or environmental samples), try to equilibrate by observed or expected target molarity, rather than by total library molarity.

We generally do NOT recommend pooling multiple samples per capture reaction for very degraded and/or rare targets (e.g. ancient DNA), or for very large targets (e.g. a WGE baitset targeting an entire genome). When working with ancient DNA specimens and small targets (e.g. mitochondrial DNA), consider diluting your probes and performing separate captures, rather than pooling multiple samples into a single capture reaction.

Target capture necessarily requires subjecting your libraries to a bottleneck, wherein target molecules are captured and therefore enriched, and non-target molecules are therefore removed. To have sufficient unique molecules for good sequencing coverage of your targets, successful captures DEPEND on the input of sufficiently complex libraries. For this reason, we recommend an input DNA amount of 100-500ng into each capture reaction, as amounts in this range typically perform very well. However MYbaits can be used with as few as 1 ng and as many as 2 µg of library. For libraries with a significant non-target component (e.g., ancient, forensic, or environmental samples), maximize the target component in each capture by using as much library as possible up to 2 µg, and consider two rounds of capture for higher percentage of reads on-target.

For best results, it is recommended that only amplified (non-PCR-free) NGS libraries are used for target capture. This provides multiple copies of each starting template molecule, increasing the chance of each individual molecule getting enriched. However if you need more starting material to reach the recommended amount, it is generally preferable to generate more library from fresh genomic DNA or a new batch of indexed library, rather than through extra amplification. This is because while some amplification is good, over-amplification risks reducing the observable complexity of your libraries through the uneven action of PCR bias, as some molecules will become relatively more abundant while others become rare. This is also true for manipulating your libraries after capture: amplify your post-capture libraries the minimum number of cycles necessary to reach the molarity required by your sequencing facility.

We cannot synthesize mixed bases, only A/T/C/G bases. If there are ambiguous bases (except for “N”) in your sequences, we will replace them with a single candidate base (e.g. C or T for “Y”) before bait synthesis.

If there are “N” bases in your sequences, we will skip over these ambiguities by default when we design baits. If you do not want this, you should replace them with putative sequence according to your best knowledge — for example, fill in those positions with “best guess” sequence from another allelic or species variant, if possible. If this is not possible, then you can instruct us to replace them with a filler base (T) prior to bait design. Using filler bases is appropriate for singleton or a couple of Ns, however long stretches of unknown sequence should just be omitted outright because they do not make any useful contribution to your bait design.

If you are using transcriptome sequences for your bait design, you may or may not know the location of the exon boundaries. However, this is not necessarily a problem for bait design, since we will typically design overlapping baits tiled across the full sequence. Any baits spanning across exon boundaries may not work well, but they will have neighboring baits which will still function. However any short exons (below the bait length) may not be recoverable unless they can be “padded” with true genomic (intronic) sequence.

Your decision whether to include >1 bait variant to represent additional diversity for a given region should depend on (1) the amount of diversity you want to have the ability to capture and (2) the maximum number of unique probe sequences that you want to purchase.

The ability of a given bait to hybridize to a target sequence will necessarily be dependent on the hybridization & washing conditions that you choose. Under the standard capture conditions, it is generally expected that a bait should be able to capture sequences of at least 5-10% local nucleotide divergence. Therefore, for example, it is normally NOT considered necessary to include probes for both allelic variants of a singleton SNP in a bait design, since a single bait should be able to capture both. However if you have many SNPs within a small window, you may wish to include >1 representative haplotype within your baitset. Please note that we cannot synthesize ambiguities.

That being said, the specific performance outcome of YOUR custom baitset, samples, and experimental conditions cannot be directly predicted. Target capture parameters such as sequence content of your custom baitset (e.g. GC% range, secondary structure), bait-to-bait interactions, and hybridization & washing performance will all impact capture outcomes. Additional experimental factors such as library quality, amplification parameters, multiplexing level, and sequencing depth will also be of critical relevance.

Yes! As long as we receive written permission from the original designer(s) (if it is not your kit), you can re-order any past design that we have manufactured. We can usually provide such re-orders within ~2 weeks of ordering. Please no rush orders.

Any design requiring from 1 to 20,000 probes falls into our smallest “myBaits-1” tier baitset scale, therefore there is no reduced price for ordering smaller probesets. However please note that probes for all custom designs are provided at the same concentration, regardless of the number of individual baits in the design.
16 reactions is now our minimum custom kit size (for both new and repeat orders). We cannot provide discounted kits for fewer reactions.

Ordering Information

Catalog # Description Quantity Price Contact Us
300116 myBaits Custom, designs with 1-20K probes 16 $3600 Order Now
300148 myBaits Custom, designs with 1-20K probes 48 $5990 Order Now
300196 myBaits Custom, designs with 1-20K probes 96 $9120 Order Now
300216 myBaits Custom, designs with 20-40K probes 16 $4850 Order Now
300248 myBaits Custom, designs with 20-40K probes 48 $7490 Order Now
300296 myBaits Custom, designs with 20-40K probes 96 $11280 Order Now
300316 myBaits Custom, designs with 40-60K probes 16 $6100 Order Now
300348 myBaits Custom, designs with 40-60K probes 48 $8990 Order Now
300396 myBaits Custom, designs with 40-60K probes 96 $13440 Order Now
300416 myBaits Custom, designs with 60-80K probes 16 $7350 Order Now
300448 myBaits Custom, designs with 60-80K probes 48 $10490 Order Now
300496 myBaits Custom, designs with 60-80K probes 96 $15600 Order Now
300516 myBaits Custom, designs with 80-100K probes 16 $8600 Order Now
300548 myBaits Custom, designs with 80-100K probes 48 $11990 Order Now
300596 myBaits Custom, designs with 80-100K probes 96 $17760 Order Now
300616 myBaits Custom, designs with 100-120K probes 16 $10100 Order Now
300648 myBaits Custom, designs with 100-120K probes 48 $13490 Order Now
300696 myBaits Custom, designs with 100-120K probes 96 $19480 Order Now
300716 myBaits Custom, designs with 120-140K probes 16 $11600 Order Now
300748 myBaits Custom, designs with 120-140K probes 48 $14990 Order Now
300796 myBaits Custom, designs with 120-140K probes 96 $21220 Order Now
300816 myBaits Custom, designs with 140-160K probes 16 $13100 Order Now
300848 myBaits Custom, designs with 140-160K probes 48 $16490 Order Now
300896 myBaits Custom, designs with 140-160K probes 96 $22940 Order Now
300916 myBaits Custom, designs with 160-180K probes 16 $14600 Order Now
300948 myBaits Custom, designs with 160-180K probes 48 $17990 Order Now
300996 myBaits Custom, designs with 160-180K probes 96 $24670 Order Now
301016 myBaits Custom, designs with 180-200K probes 16 $16100 Order Now
301048 myBaits Custom, designs with 180-200K probes 48 $19490 Order Now
301096 myBaits Custom, designs with 180-200K probes 96 $26400 Order Now

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