Patent Publication Number: US-2023134044-A1

Title: Thermal cycler systems and methods of use

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation application of U.S. application Ser. No. 16/590,459, filed Oct. 2, 2019, which is a divisional application of U.S. application Ser. No. 15/387,614, filed Dec. 21, 2016 (now U.S. Pat. No. 10,471,432), which claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent Application Nos. 62/372,876 filed on Aug. 10, 2016 (now expired) and to 62/270,716 filed on Dec. 22, 2015 (now expired), each of which are incorporated herein by reference in their entirety. 
    
    
     TECHNICAL FIELD 
     The present invention relates generally to thermal cycler systems and methods of using same. 
     Introduction 
     Testing of biological or chemical samples often requires a device for repeatedly subjecting multiple samples though a series of temperature cycles. To prepare, observe, test, and/or analyze an array of biological samples, one example of an instrument that may be utilized is a thermal cycler or thermocycling device, such as an end-point polymerase chain reaction (PCR) instrument or a quantitative, or real-time, PCR instrument. Such devices are used to generate specific temperature cycles, i.e. to set predetermined temperatures in the reaction vessels to be maintained for predetermined intervals of time. 
     Generally, thermal cycler systems include a sample block that has a plurality of reaction regions or sample block wells and that is configured to receive a plurality of samples contained in sample wells of a sample holder. The samples may be sealed within the wells of the sample holder via a lid, cap, sealing film or any other sealing mechanism between the wells and a heated cover. A variety of sample holders are used in thermal cycler systems including, for example, a multi-well microtiter plate, a micro card, or a through-hole array. Due to the variety of available sample holders, thermal cycler systems are often designed to be compatible with more than one type of sample holder. For example, sample blocks may be configured to receive a sample holder having either a full skirt or a semi-skirt. A full-skirted sample holder has skirting that generally extends on at least two opposite sides of the sample holder to the bottom portions of the sample wells, while the skirting of the semi-skirted sample holder leaves lower portions of the sample wells exposed. Designing a thermal cycler system compatible with sample holders having different designs often leads to inefficiencies depending on the actual sample holder used. To perform the PCR process successfully, efficiently, and accurately, these inefficiencies should be minimized to the greatest extent possible. 
     There is an increasing need to provide improved thermal cycler systems that address one or more of the above drawbacks. 
     SUMMARY 
     In accordance with one embodiment, a thermal cycler system for use with a sample holder configured to receive a plurality of samples includes a sample block having an upstanding peripheral side wall and being configured to receive the sample holder and an adaptor having an upstanding peripheral side wall configured to be positioned about the peripheral side wall of the sample block. When the peripheral side wall of the adaptor is positioned about the peripheral side wall of the sample block and the sample holder is received in the sample block, the peripheral side wall of the adaptor extends in an upward direction toward the sample holder. 
     In accordance with another embodiment, an adaptor configured to be positioned about a sample block, the sample block including an upstanding peripheral side wall and being configured to receive a sample holder, includes an upstanding peripheral side wall. When the peripheral side wall of the adaptor is positioned about the peripheral side wall of the sample block and the sample holder is received in the sample block, the peripheral side wall of the adaptor extends in an upward direction toward the sample holder. 
     Various additional features and advantages of the invention will become more apparent to those of ordinary skill in the art upon review of the following detailed description of the illustrative embodiments taken in conjunction with the accompanying drawings. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate embodiments of the invention and, together with a general description of the invention given above, and the detailed description given below, serve to explain the invention. 
         FIG.  1    is a perspective view of a thermal cycler system according to one embodiment showing an adaptor and sample holder positioned about the sample block. 
         FIG.  2    is an exploded view of the thermal cycler system of  FIG.  1    showing the sample holder removed from the sample block. 
         FIG.  3    is an exploded view of the thermal cycler system of  FIG.  1    showing the adaptor and insulation components removed from the sample block without the sample holder and showing a portion of the housing in cross-section. 
         FIG.  4 A  is a cross-sectional view of a portion of the thermal cycler system of  FIG.  1    and the sample holder. 
         FIG.  4 B  is a cross-sectional view of the portion of the thermal cycler system of  FIG.  4 A  showing the sample holder positioned on the adaptor and the sample block. 
         FIG.  5    is a cross-sectional view of a portion of the thermal cycler system of  FIG.  1    and a sample holder having a different design than the sample holder of  FIG.  4 A . 
         FIG.  6 A  is a perspective view of a sample block above a drip pan with wire form springs. 
         FIG.  6 B  is a lengthwise side view of the sample block and drip pan of  FIG.  6 A . 
         FIG.  6 C  is a widthwise side view of the sample block and drip pan of  FIG.  6 A . 
     
    
    
     DETAILED DESCRIPTION 
     Referring to  FIGS.  1 - 3   , a thermal cycler system  10  is shown constructed in accordance with an illustrative embodiment of the present invention. The thermal cycler system  10  includes an outer housing  12 , a sample block  14 , and a drip pan  16 . The sample block  14  includes a plurality of cavities  18  and is configured to be loaded with a correspondingly shaped sample holder  20  containing a plurality of biological or biochemical samples in a plurality of sample wells  22 . The drip pan  16  is designed to seal components of the thermal cycler system  10 , such as a thermal block assembly (not shown), from environmental conditions above the drip pan  16 . A thermal block assembly may include, for example, a heating and cooling element and a heat exchanger or heat sink for heating and cooling the biological or biochemical samples during the PCR process. The thermal cycler system  10  is described in greater detail below. 
     Still referring to  FIGS.  1 - 3   , the thermal cycler system  10  includes an access area  24  for the sample holder  20  to be inserted and removed. In various embodiments, the access area  24  is configured to include enough open space for a robotic arm of a lab automation system (not shown) to position the sample holder  20  on the sample block  14 . Additionally, the thermal cycler system  10  is configured to be compatible with a full-skirted sample holder (not shown). The space required for the manipulation of the sample holder  20  by a robotic arm poses a problem when the sample holder is semi-skirted rather than full-skirted. In that regard, when a semi-skirted sample holder  20  is received by the sample block  14 , a peripheral wall  26  of the sample block  14  is exposed. Thus, the sample block  14  is vulnerable to an external air draft, which may severely affect the consistent thermal performance of the thermal cycler system  10 . Accordingly, in one embodiment, the thermal cycler system  10  includes an adaptor  28 , which is described in greater detail below. 
     The exemplary thermal cycler system  10 , unless otherwise indicated, is described herein using a reference frame in which the sample holder  20  may be loaded in the front of the thermal cycler system  10  and may be positioned above the sample block  14 . Consequently, as used herein, terms such as lateral, forward, backward, downward, upward, beneath, and above used to describe the exemplary thermal cycler system  10  are relative to the chosen reference frame. The embodiments of the present invention, however, are not limited to the chosen reference frame and descriptive terms. Those of ordinary skill in the art will recognize that the descriptive terms used herein may not directly apply when there is a change in reference frame. Nevertheless, the relative terms used to describe embodiments of the thermal cycler system  10  are to merely provide a clear description of the embodiments in the drawings. As such, the relative terms lateral, forward, backward, downward, upward, beneath, and above are in no way limiting the present invention to a particular location or orientation. 
     With reference now to  FIGS.  3  and  4 A , the exemplary sample block  14  is shown in more detail. The sample block  14  includes a base  30  and the upstanding peripheral side wall  26 , which encloses the plurality of cavities  18 . As described above, the plurality of cavities  18  are configured to receive the plurality of correspondingly shaped sample wells  22  of the sample holder  20 . In the illustrative embodiment, the sample block  14  includes 96 cavities  18 . In such an embodiment, the sample holder  20  may be a 96-well microtiter plate. It should be recognized that the sample block  14  and the sample holder  20  may have alternate configurations. For example, the sample holder  20  may be, but is not limited to, any size multi-well plate, card or array including, but not limited to, a 24-well microtiter plate, 50-well microtiter plate, a 384-well microtiter plate, a microcard, a through-hole array, or a substantially planar holder, such as a glass or plastic slide. 
     Still referring to  FIGS.  3  and  4 A , the exemplary drip pan  16  is shown in more detail. The drip pan  16  forms a seal between the sample block  14  and the drip pan  16  to isolate thermoelectric components (not shown) from environmental conditions above the sample block  14  and the drip pan  16 . In particular, the drip pan  16  prevents any sample that may splash out of the sample wells  22  from reaching the sensitive electronic components of the thermal block assembly (not shown). The drip pan  16  includes a side wall  32  and a bottom surface  34 . In one embodiment, the drip pan  16  is configured to receive the adaptor  28 . Further, the drip pan  16  may be configured to secure a lateral position of the adaptor  28  relative to the drip pan  16 . In that regard, when the adaptor  28  is received by the drip pan  16 , the side wall  32  of the drip pan  16  prevents lateral movement of the adaptor  28 . 
     With reference again to  FIGS.  3  and  4 A , the adaptor  28  is shown in more detail. The adaptor  28  includes a deck portion  36  including a plurality of apertures  38 . The plurality of apertures  38  is configured to allow the array of sample wells  22  of the sample holder  20  to extend therethrough when the adaptor  28  is positioned about the sample block  14  and sample holder  20  is received by the sample block  14  (shown in  FIG.  4 B ). A perimeter  40  of the deck portion  36  is formed with an upstanding peripheral side wall  42  extending downwardly beneath the deck portion  36 . The upstanding peripheral side wall  42  is configured to be positioned about the peripheral side wall  26  of the sample block  14 . When the peripheral side wall  42  of the adaptor  28  is positioned about the peripheral side wall  26  of the sample block  14  and the sample holder  20  is received in the sample block  14 , the peripheral side wall  42  of the adaptor  28  extends in an upward direction toward the sample holder  20  (described below). In other words, the peripheral side wall  42  of the adaptor  28  may extend in a direction from the base  30  of the sample block  14  towards a deck portion  44  of the sample holder  20 . In this manner, the peripheral side wall  42  of the adaptor  28  is configured to protect the peripheral side wall  26  of the sample block  14  from undesirable contact with air flow during the PCR process. It should be recognized that the peripheral side wall  42  of the adaptor  28  may be a continuous or a discontinuous side wall. In other words, in various embodiments, the peripheral side wall  42  may comprise one or more wall segments. 
     Still referring to  FIGS.  3  and  4 A , the perimeter of the upstanding peripheral side wall  42  of the adaptor  28  includes a lip  46  extending therefrom. The lip  46  is configured to be received by the drip pan  16 . When the lip  46  is received by the drip pan  16 , the lateral position of the adaptor  28  may be secured by the drip pan  16 . In one embodiment, an insulation component  47  may be positioned between the drip pan  16  and the lip  46  of the adaptor  28 . The insulation component  47  may be adhered to the drip pan  16 , for example. Additionally, in one embodiment, insulation components  49  may be coupled to the deck portion  36  of the adaptor  28 . The insulation components  49  may aid in preventing draft air from the front and back of the thermal cycler system  10 . In addition, the insulation components  49  may also act as a secondary uniform force on the bottom of the sample holder  20  to aid in the ejection of the sample holder  20  after the PCR process is complete. The insulation components  47 ,  49  may be made of BISCO.RTM. HT-800 Medium Cellular Silicone available from Rogers Corporation in Rogers, Conn. for example. While the adaptor  28  is shown as including the deck portion  36  and the lip  46 , it should be recognized that other configurations of the adaptor  28  are possible. For example, an adaptor according to one embodiment may not include a deck portion or a lip. Further, in one embodiment, the adaptor  28  may be configured to accommodate a full-skirted sample holder (not shown). In an embodiment where the adaptor  28  is configured to accommodate only semi-skirted sample holders, the adaptor  28  may be positioned about the sample block  14  before the sample holder  20  is loaded. For subsequent runs, no user intervention or replacement is necessary until the user wants to use a full-skirted sample holder. 
     Referring again to  FIGS.  2  and  3   , in one embodiment, the drip pan  16  includes a plurality of ejector mechanisms  48 . While the illustrated embodiment shown in  FIG.  3    depicts four ejector mechanisms  48 , other embodiments may employ a single ejector mechanism  48  or a suitable number of a plurality of ejector mechanisms  48 . The ejector mechanisms  48  may allow for easier removal of the sample holder  20  after the PCR process is complete. Each ejector mechanism  48  may comprise one or more springs that are compressed when a sample holder  20  is placed onto the sample block. As illustrated within the embodiments shown in  FIGS.  2  and  3   , the springs are contained within a housing component of the ejector mechanisms  48 , but other embodiments may employ different housings or no housing at all. Additionally, the number and size of ejector mechanisms  48  (and the number of size of springs within ejector mechanisms  48 ) will vary depending on the size and format of drip pan  16 , sample block  14 , sample holder  20  and any adaptor  28  that is employed. To account for the ejector mechanisms  48 , the adaptor  28  includes a plurality of openings  50  configured to allow the ejector mechanisms  48  to extend therethrough in order to make contact with sample holder  20  for the purposes of ejection. The openings  50  may extend beyond the perimeter of the peripheral side wall  42 . Therefore, the peripheral side wall  42  may include extensions  52 . When the ejector mechanisms  48  extend through the openings  50 , the extensions  52  of the peripheral side wall  42  at least partially surround the ejector mechanisms  48 . Further, the perimeter  40  of the deck portion  36  may extend inward from the perimeter of the peripheral side wall  42 . In the illustrated embodiment, the openings  50  extend across a section of the deck portion  36  that may otherwise include apertures  38 . Accordingly, the openings  50  may be configured to allow one or more of the sample wells  22  of the sample holder  20  to extend therethrough when the sample holder  20  is positioned adjacent the adaptor  28 . Further, a deck portion segment  54  of the deck portion  36  may extend to the perimeter of the peripheral side wall  42  between the openings  50 . In this manner, the peripheral side wall  42  acts to protect the sample block  14  from undesirable contact with air flow while allowing the ejector mechanisms  48  to extend through the adaptor  28 . 
     With reference to  FIGS.  6 A- 6 C , an embodiment is illustrated where drip pan  16  includes wire form springs  68  as an embodiment of ejector mechanisms  48 . In such embodiments, the springs are not contained within a housing, as depicted within the illustrated embodiment shown in  FIGS.  2 - 3   . Within the illustrated embodiment of  FIGS.  6 A- 6 C , drip pan  16  includes a wire form spring  68  on each of its four sides around where the sample block is placed. Other embodiments may include more than one wire form spring  68  per side, or only include one or more wire form springs  68  on a subset of the sides of drip pan  16  (e.g., on one side, two sides, or three sides). Additionally, one or more wire form springs  68  may be employed in combination with other ejector mechanisms  48 , such as but not limited to those described in association with the embodiments illustrated in  FIGS.  2  and  3   . 
     With further reference to  FIGS.  6 A- 6 C , embodiments employing wire form springs  68  may be configured to operate without an adaptor  28 , with sample wells  22  being inserted into cavities  18  when sample holder  20  is placed on sample block  14 . The wire form springs  68  are located on drip pan  16  such that sample holder  20  is placed on top of wire form springs  68 , which compresses the wire form springs  68 . In this fashion, wire form springs  68  can assist in ejection of sample holder  20 . The use of wire form springs  68  can be beneficial when spatial constraints may not allow the use of other ejector mechanisms  48  on one or more sides of drip pan  16 , or when the spatial constraints do not allow the use of an adaptor  28  (e.g., when spatial constraints do not allow the use of an adaptor  28  with a plurality of openings  50  through which ejector mechanisms  48  extend, as illustrated within the embodiment shown in  FIG.  3   ). Certain embodiments, including but not limited to those using an adaptor  28 , may combine wire form springs  68  with other ejector mechanisms  48  to enhance the overall ejection of sample holder  20 . Wire form springs  68  can comprise any suitable material. Non-limiting examples of suitable wire form springs  68  include music wire of 0.90 mm of SWP-B, JIS G3522 with zinc plating or chromium finishing, and also stainless steel wire springs of 0.90 mm of stainless steel 17-7 PH with precipitation hardening. Other suitable materials for wire form springs  68  include high carbon steel, carbon alloys, hard drawn steel, steel alloys, non-ferrous alloys, high temperature alloys, and other metals and alloys known in the art. 
     With further reference to  FIGS.  2  and  3   , embodiments employing a sample holder  20  in a full skirt configuration may utilize the heated cover and adaptor  28  to enhance removal of sample holder  20 . In such embodiments, when the heated cover is lowered to provide a downward force to the sample holder  20  as discussed below in reference to  FIGS.  2  and  4 A , the skirt of sample holder  20  will sit on top of and be depressed into a portion of adaptor  28 . The materials for the skirt of sample holder  20  and the adaptor  28  are chosen in such embodiments to allow the skirt to be depressed into the adaptor without damaging either component. For example, a skirt wall  62  of plastic and the corresponding portion of adaptor  28  of silicon rubber allowing for repeated use with the plastic skirt wall  62  being depressed into the silicon rubber portion of adaptor  28 . Any appropriate portion of the skirt of sample holder  20  can be depressed into adaptor  28 , such as a side or sides of sample holder  20  that do not interact with other features (for example, ejector mechanisms  48 ) to enhance removal of sample holder  20 . Removal of the heated cover removes the downward force onto sample holder  20 , thereby creating a spring cantilever force to eject sample holder  20 . In one embodiment, sample holder  20  in a full skirt configuration employs the depression of the skirt into adaptor  28  for the ejection and removal of sample holder  20 . In another embodiment, the full skirt configuration of sample holder  20  being depressed into adaptor  28  is combined with the use of ejector mechanisms (for example, the plurality of ejector mechanisms as described in the illustrated embodiment within  FIG.  3   ). In embodiments where drip pan  16  includes one or more ejector mechanisms  48  and a full skirt configuration of sample holder  20  is utilized, the skirt may be depressed into adaptor  28  along sides or portions for which there are no ejector mechanisms  48 , thereby providing ejection force (from, for example, both or either ejector mechanisms  48  or from the spring cantilever force created when the heated cover is lowered onto the sample holder) that will act on multiple sides of sample holder  20 . In reference to the illustrated embodiment of  FIG.  3   , use of a sample holder  20  with a full skirt would allow the use of ejector mechanisms  48  along the short sides of sample holder  20  to be combined with depression of the long sides of the skirt into adaptor  28  in order to provide ejection force on all four sides of sample holder  20 . Embodiments utilizing the creation of a spring cantilever force to aid in removal of sample holder  20  after lifting of the heated cover provide advantages in ensuring complete removal. The temperatures involved during thermal cycling can complicate complete removal as the heat can cause thermal warpage of sample holder  20 , such as when higher temperatures during thermocycling are employed or when sample holder  20  comprises non-hard shell materials that are more susceptible to thermal warpage. 
     With further reference to  FIG.  3   , in one embodiment, the drip pan  16  and the adaptor  28  include corresponding mating features. The corresponding mating features act as a self-locating feature to ensure the proper placement of the adaptor  28 . In the illustrated embodiment, the side wall  32  of the drip pan  16  includes projections  56 , and the lip  46  of the adaptor  28  includes recesses  58 . The projections  56  are configured to engage the recesses  58  when the adaptor  28  is received by the drip pan  16 . In that manner, the adaptor  28  is unlikely to be displaced if it is accidently hit by a robotic arm (not shown) during operation. 
     With reference now to  FIGS.  2  and  4 A , the exemplary sample holder  20  is shown in more detail. The sample holder  20  includes a deck portion  44  that supports the plurality of sample wells  22  in a regular array or matrix. The deck portion  44  serves to connect the adjacent sample wells  22  near to or at the top of each sample well  22  and to hold them in the desired matrix. The sample wells  22  are designed with generally thin walls to allow heat transfer to take place between the sample block  14  and the contents of the well. A perimeter  60  of the deck portion  44  is commonly formed with a skirt wall  62  extending downwardly beneath the deck portion  44 . The skirt wall  62  may be integrally formed with the deck portion  44  during molding of the sample holder  20  and generally forms a continuous wall of constant height around the sample holder  20 . In the illustrated embodiment, the sample holder  20  is semi-skirted meaning the skirt wall  62  does not extend to the bottom of the sample wells  22 . The skirt wall  62  lends stability to the sample holder  20  when it is placed on a surface and some rigidity when the sample holder  20  is being handled. The sample holder  20  is configured to be positioned over the sample block  14  and the adaptor  28 . A heated cover (not shown) may provide a downward force to the sample holder  20 . The downward force provides vertical compression between the sample holder  20 , the sample block  14 , and the other components of thermal block assembly (not shown), which improves thermal contact between the sample block  14  and the sample holder  20  to heat and cool the samples in the sample wells  22 . The heated cover may also prevent or minimize condensation and evaporation above the samples contained in the sample wells  22 , which can help to maintain optical access to samples. 
     Referring again to  FIGS.  3  and  4 A , the sample wells  22  of the sample holder  20  are configured to receive a plurality of samples. The sample wells  22  may be sealed within the sample holder  20  via a lid, cap, sealing film or other sealing mechanism between the sample wells  22  and the heated cover (not shown). The sample wells  22  in various embodiments of a sample holder  20  may include depressions, indentations, ridges, and combinations thereof, patterned in regular or irregular arrays formed on the surface of the sample holder  20 . Sample or reaction volumes can also be located within wells or indentations formed in a substrate, spots of solution distributed on the surface a substrate, or other types of reaction chambers or formats, such as samples or solutions located within test sites or volumes of a microfluidic system, or within or on small beads or spheres. Samples held within the sample wells  22  may include one or more of at least one target nucleic acid sequence, at least one primer, at least one buffer, at least one nucleotide, at least one enzyme, at least one detergent, at least one blocking agent, or at least one dye, marker, and/or probe suitable for detecting a target or reference nucleic acid sequence. 
     With reference to  FIGS.  4 A and  4 B , the configuration of the sample block  14 , the adaptor  28 , and the sample holder  20  is shown in more detail. A user may position the adaptor  28  so that the peripheral side wall  42  of the adaptor  28  is positioned about the peripheral side wall  26  of the sample block  14 . Some of the cavities  18  of the sample block  14  are aligned with the apertures  38  of the adaptor  28 , while other cavities  18  are aligned with the openings  50  (not shown in the cross-section of  FIG.  4 B ). Next, the user may position the sample holder  20  on the sample block  14 . The sample wells  22  of the sample holder  20  extend through the apertures  38  or openings  50  of the adaptor  28  and into the cavities  18  of the sample block  14 . The deck portion  36  of the adaptor  28  may be configured to maintain proper engagement between the sample wells  22  of the sample holder  20  and the cavities  18  of the sample block  14 . For example, the thickness of the deck portion  36  of the adaptor  28  may be designed so as to allow the sample wells  22  to properly extend into the cavities  18 . If the thickness of the deck portion  36  is too large and the sample wells  22  are not properly engaged with the cavities  18 , the heat transfer between the sample wells  22  and the cavities  18  may be significantly impacted leading to process inefficiencies. When the sample holder  20  is received by the sample block  14 , the peripheral side wall  42  of the adaptor  28  extends in an upward direction toward the sample holder  20 . In other words, the peripheral side wall  42  of the adaptor  28  extends in a direction from the base  30  of the sample block  14  towards the deck portion  44  of the sample holder  20 . Further, the peripheral side wall  42  extends laterally in a space between the skirt wall  62  of the sample holder  20  and the peripheral side wall  26  of the sample block  14 . In this manner, the peripheral side wall  42  of the adaptor  28  protects the peripheral side wall  26  of the sample block  14  from undesirable air flow that would interfere with the heat transfer during the PCR process. 
     Advantageously, the configuration of the adaptor  28  allows for the thermal cycler system  10  to be compatible with sample holders that vary in design. The design of the peripheral side wall of commercially available sample holders may vary, for example. With reference to  FIG.  5   , a sample holder  64  is shown positioned on the adaptor  28 . As can be seen, the sample holder  64  has a design that differs from the design of the sample holder  20  shown in  FIGS.  4 A and  4 B . Thus, the adaptor  28  is configured to receive a variety of sample holders. 
     While the present invention has been illustrated by the description of specific embodiments thereof, and while the embodiments have been described in considerable detail, it is not intended to restrict or in any way limit the scope of the appended claims to such detail. The various features discussed herein may be used alone or in any combination. Additional advantages and modifications will readily appear to those skilled in the art. The invention in its broader aspects is therefore not limited to the specific details, representative apparatus and methods and illustrative examples shown and described. Accordingly, departures may be made from such details without departing from the scope or spirit of the general inventive concept.