DESC:CROSS-REFERENCE TO RELATED APPLICATIONS AND PRIORITY
The present application does claim priority from its provisional application filed on 11th November 2022 under the application number of 202221064497.

TECHNICAL FIELD
The present subject matter described herein, in general, relates to an integrated device for processing biological samples. More particularly, the present invention relates to the integrated device to automate ‘Sample-to-Result’ operations of DNA/RNA extraction and PCR Amplification of a single sample to detect, quantify, and identify various parameters.

BACKGROUND
The subject matter discussed in the background section should not be assumed to be prior art merely as a result of its mention in the background section. Similarly, a problem mentioned in the background section or associated with the subject matter of the background section should not be assumed to have been previously recognized in the prior art. The subject matter in the background section merely represents different approaches, which in and of themselves may also correspond to implementations of the claimed technology.
Molecular diagnostics has emerged as a field that offers the promise of early disease detection, potentially before symptoms have manifested. Molecular diagnostic testing is used to detect: Inherited disorders, Acquired disorders, Infectious diseases and Genetic predisposition to health-related conditions. With high accuracy and fast turnaround times, molecular diagnostic tests have the potential to reduce the occurrence of ineffective health care services, enhance patient outcomes, improve disease management and individualized patient care. Many of the techniques in molecular diagnostics are based on the detection and identification of specific nucleic acids, both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), extracted and amplified from a biological specimen (such as blood, saliva or sputum).
Molecular diagnostics testing is often practiced in centralized laboratories, which requires trained personnel, regulated infrastructure, and expensive, high throughput instrumentation. Some known high throughput laboratory equipment generally processes many samples at a time, therefore central lab testing is often done in batches. The known methods for processing test samples typically include processing all samples collected during a time period (e.g., a day) in one large run, resulting in a turn-around time of many hours to days after the sample is collected. Moreover, such known equipment and methods are designed to perform certain operations under the guidance of a skilled technician who adds reagents, overseas processing, and moves samples from step to step. Thus, the known laboratory tests and methods often take considerable time and are very expensive. Further the molecular diagnostic testing, even performed by skilled technicians, also entails human error.
Although some known laboratory-based molecular diagnostics test methods and equipment offer flexibility (e.g., the ability to test for multiple different indications), such methods and equipment are not easily adaptable for point of care (“POC”) use or “near-patient testing” use by an untrained user. Specifically, such known devices and methods are complicated to use and include expensive and sophisticated components. Further, the lab technician needs to perform the DNA/RNA extraction process manually, due to the lack of a single sample testing machine. Thus, there exists a need for a compact “near-patient testing” device that works with one sample at a time.

OBJECTIVES OF THE PRESENT INVENTION
Some of the objects of the present disclosure, which at least one embodiment herein satisfies are listed herein below.
The main object of the present disclosure is to provide an integrated device for processing biological samples.
Another objective of the present disclosure is to provide an integrated device to automate ‘Sample-to-Result’ operations of DNA/RNA extraction and PCR amplification of a single sample to detect, quantify, and identify various parameters.
Yet another objective of the present invention is to provide a portable and compact, fully automated cartridge-based device that automates ‘Sample-to-Result’ operations of integrating DNA/RNA extraction and PCR Amplification of a single sample.
SUMMARY
This summary is provided to introduce concepts related to an integrated miniaturized device to automate ‘Sample-to-Result’ operations of integrating DNA/RNA extraction and PCR Amplification of a single sample, and the concepts are further described below in the detailed description. This summary is not intended to identify essential features of the claimed subject matter, nor it is intended for use in determining or limiting the scope of the claimed subject matter.
In one embodiment of the present invention disclosure, a portable, fully automated cartridge-based device which automates ‘Sample-to-Result’ operations of integrating DNA/RNA extraction and PCR Amplification of a single sample. The disclosed cartridge-based device may have a capability to perform operations on a single sample. The device may accept sample types, including but not limited to, Plasma, Tissue, Sputum, swabs, and more. Further, the device is preloaded with a cartridge features six chambers to perform Extraction and Amplification of DNA. The device automatically extracts and purifies the DNA/RNA and performs the Polymerase Chain Reaction (PCR) consecutively. The PCR results are analysed using a branched optical fibre-based detection technique. The final PCR readings are displayed in real-time on a digital screen.
In another embodiment of the present invention disclosure, a process of the cartridge-based device including a DNA/RNA extraction process and a PCR Amplification process is disclosed. The process of the cartridge-based device is executed by six modules of the cartridge-based device. The six modules comprise: Module 1: Cartridge Tray
Module 2: Syringe Module, Syringe Up-Down Module
Module 3: Tip Discard Mechanism
Module 4: Thermoshaker Module
Module 5: Heating Lid Mechanism
Module 6: Detection Mechanism
The DNA/RNA extraction process is executed by using Module 1, 2, 3, 4 and the PCR Amplification process is executed by using Module 5 and 6. Further, the detailed information about components and working of all Modules 1-6 will be described under Detailed Description.

BRIEF DESCRIPTION OF DRAWINGS
The detailed description is described with reference to the accompanying Figures. In the Figures, a reference number identifies the Figure in which the reference number first appears. The same numbers are used throughout the drawings to refer to features and components.
Figure 1a illustrates a first perspective view of a cartridge-based device, in accordance with an embodiment of the present disclosure.
Figure 1b illustrates a second perspective view of the cartridge-based device, in accordance with an embodiment of the present disclosure.
Figure 2 illustrates a flow diagram 200 for the process of DNA/RNA extraction, in accordance with an embodiment of the present disclosure.
Figure 3 illustrates a flow diagram 300 for process of PCR Amplification, in accordance with an embodiment of the present disclosure.
Figure 4 illustrates multiple views of the Syringe Module, in accordance with an embodiment of the present disclosure.
Figure 5 illustrates multiple views of the Detection Module, in accordance with an embodiment of the present disclosure.
Figure 6 illustrates multiple views of the Thermo-Shaker Module, in accordance with an embodiment of the present disclosure.

DETAILED DESCRIPTION
Reference throughout the specification to “various embodiments,” “some embodiments,” “one embodiment,” or “an embodiment” means that a particular feature, structure, or characteristic described in connection with the embodiment is included in at least one embodiment. Thus, appearances of the phrases “in various embodiments,” “in some embodiments,” “in one embodiment,” or “in an embodiment” in places throughout the specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures or characteristics may be combined in any suitable manner in one or more embodiments.
Referring to Figure 1a, a perspective view of a cartridge-based device 101, is illustrated in accordance with an embodiment of the present disclosure. The cartridge-based device 101 is a portable and fully automated device which automates ‘Sample-to-Result’ operations of integrating DNA/RNA extraction and PCR Amplification of a single sample. The cartridge-based device 101 may have a capability to perform operations on a single sample. The device 101 may accept sample types, including but not limited to, Plasma, Tissue, Sputum, swabs and more. The cartridge-based device 101 comprises a Cartridge Tray 101, a Syringe Module 102, a Syringe up-down mechanism 103, a Tip Discard mechanism 104, a Thermo-Shaker Module 105, a Heating Lid mechanism 106, a Detection Module 107, an Electronics 108, a cooling fan 109, a base plate 110, a Magnet mechanism 111 (as illustrated in Figure 1b) and one or more motors 112 (as illustrated in Figure 1b).
The Cartridge Tray 101 may encase a removable rotating cartridge deck. The removal and insertion of the rotating cartridge deck may be fully automated and may be access controlled via a digital screen (not illustrated) associated with the Cartridge Tray 101. The removable rotating cartridge deck may comprise a 5ml-….ml reaction tube and five chambers (not illustrated). All the main reactions required for DNA/RNA extraction are carried out on this rotating cartridge deck. The five chambers of the rotating cartridge deck may comprise:
1) Chamber 1: The chamber 1 may have 10 wells having the reagents/chemicals required for DNA/RNA extraction procedure
2) Chamber 2: The chamber 2 may have 6 wells having the master mix solutions required for the PCR reactions.
3) Chamber 3: The chamber 3 may contain 10 Tip holding wells.
4) Chamber 4: The chamber 4 may have a single piercing plastic needle well.
5) Chamber 5: The chamber 5 may have 6 wells housing PCR tubes which will further undergo Denaturation, Annealing, and Extension steps of PCR.
In one embodiment, a cartridge may have a shape of circular cartridge. The cartridge may be made of Plastic/ Polyphenylene Ether (PPE) material. The dimensions of the cartridge may be not more than 80 mm tall and not more than 100 mm diameter. The cartridge may comprise a two-latch mechanism with interlocking latches which may secure the cartridge in place. The cartridge may be apt according to a protocol selected from one or more protocols. Protocols are selected based on the diagnostic kits developed for detecting or diagnosing the markers including and not limiting to onco-markers, biomarkers and infectious disorders, genetic disorders and similar life-science related diagnosis. Further, a Thermal Cycler is placed under the cartridge deck in the tray. The basal parts of the PCR tubes may be exposed to the thermal cycler.
In one more embodiment, a cartridge may have a shape of square or rectangular and it is made of plastic/ polyphenylene ether material.
In one embodiment, the Syringe Module 102 and the Syringe up-down mechanism 103 may help in Piercing the aluminium foils covered wells and aspiring/dispensing the reagents and chemicals in the assigned wells. The Tip Discard mechanism 104 may help to ensure that the used tip is appropriately discarded in the original well from which it was picked. Further, the Thermo-Shaker Module 105 may be used to heat the wells while shaking them to achieve homogenization. The Heating Lid mechanism 106 may be used to regulate the temperature of the PCR tubes. Further, the Detection Module 107 may be used for the Analysis and Viewing of the final PCR results. The Electronics 108 may comprise processing chips, control units, Display screen or more. The Electronics 108 may be used to receive input from the user and provide instructions to various modules of the cartridge-based device 101. The cooling fan 109 may be used to cool down the PCR tubes. The base plate 110 may be used to hold the multiple modules of the cartridge-based device 101. The magnet mechanism 111 is coordinating with the Thermo-Shaker Module 105 for extraction of DNA/RNA. Further, the one or more motors 112 may be used to power the multiple modules of the cartridge-based device 101.
Referring to Figure 2, the process flow 200 of the cartridge-based device 101 for DNA/RNA extraction is illustrated, in accordance with an embodiment of the present disclosure. The process flow 200 of the cartridge-based device 101 may use modules such as the Cartridge Tray 101, the Syringe Module 102, the Syringe up-down mechanism 103, the Tip Discard mechanism 104, and the Thermo-Shaker Module 105.
In an embodiment of the present disclosure the cartridge-based device is portable and lightweight and hence easy to carry. The weight of the device is ranging from 10 to 50 kg. As per the embodiment of the present invention, the weight of the device is less than 10kg.
In an embodiment of the present disclosure, the cartridge-based device as disclosed herein provides accurate results in a shorter period such as less than 90 minutes.
In a particular embodiment of the present invention, the device provides accurate results in a shorter period depending on the protocol selected.
The system as disclosed herein can be used for but not limited to the identification of COVID-19, infectious diseases, genetic disorders, tuberculosis, oncology and genetic markers, onco-markers, life science kits and many more like this.
The process flow comprises step 201 for selecting a protocol from the one or more protocol according to the sample and the cartridge. The protocol selection may be performed automatically or may be performed manually by an operator. After the selection of the protocol, the process will begin automatically.
In step 202 the sample is manually added in the reaction tube with the adequate buffers.
In step 203, the reaction tube may be placed in the Thermo-Shaker module 105. The Thermo-Shaker module 105 is enabled to heat the sample and shake it to achieve homogenization.
In step 204, the Syringe Module 102 by the help of a Tip holder may take up a piercing needle or tip and pierce the extraction wells already sealed with aluminium foils.
In step 205, the piercing tip may return to its original position after piercing.
In step 206, the Syringe Module 102 by the help of the Tip holder chooses another piercing tip and pierce the PCR mix well using the piercing tip.
In step 207, the piercing tip may return to its original position after piercing.
Further, in step 208, the tip holder may use the Tip Discard mechanism 104 to drop the used tip into the same well.
In step 209, the Thermo-Shaker Module 105 may be used to mix and heat all of the reagents and samples in the reaction, and magnetic bead-based technology 111 is used for the extraction of DNA/RNA. The Magnet for the same is provided from the side. Further, a fresh tip will be used for the recovery of pure DNA or RNA.
In step 210, the buffer and the pure DNA/RNA are eluted in a defined well, based on the selected protocol.
Referring to Figure 3, the process flow 300 of the cartridge-based device 101 for PCR Amplification is illustrated, in accordance with an embodiment of the present disclosure.
In step 301 the sealed PCR mix wells may be pierced using the piercing needle or tip.
In step 302, DNA/RNA may be aspirated and dispensed in the master mix, using a new tip. Further a new tip may be used for each well to dispense the mixture (from the six wells) into the corresponding PCR tubes.
In step 303, the PCR tubes' caps may be successively pressed (or closed) by the tip holder.
In step 304, heating lids (110°C) may be applied uniformly, by using Heating Lid mechanism 106, to all 6 PCR tubes' tops. Further, to maintain the temperature at the neck of the PCR tubes, a neck heating lid may be placed around the tubes.
In Step 305, a connected, branched optical fiber holder may be positioned above the heating lid. The branched optical fiber may be automatically positioned on top of the caps after the heated lid has been attached to them.
In step, 306 placing the PCR tubes in the thermal cycler. A Peltier belt mechanism may assist in heating and cooling required for the PCR process. To counteract the Peltier's heat, a heat sink is positioned beneath it. A three-stage PCR procedure is carried out in cycles. Denaturation, or the separation of the DNA molecule's two strands, is the first stage. This may be done by raising the initial temperature. Every strand serves as a foundation for another one to be constructed. The temperature is lowered in the second stage so that the primers can anneal to the template. The third stage involves increasing the temperature slightly, at which point the DNA polymerase starts to anneal the primer ends and add nucleotides. After each cycle, the number of copies doubles. The number of cycles vary with the selected protocol. 24 targets can be achieved from a single sample.
In step 307, LED signals from the rotating Detection Module 107 may be transmitted to the PCR tubes by the branched optical fibres from the top, and the Detection Module 107 may receive the signals via the branched optical fibres.
In step 308, the received optical signals may be transformed into electrical (signal) impulses and then fluorescence as graphs may be shown on the digital screen. The operator may then perform a manual analysis of the data.
In step 309, flexible customization to the data may be performed, via different available programming options, by using the Simplest User Interface (UI) on the screen.
In step 310, the used cartridge may be Disposed-off and UV illumination may be applied to sterilize the cartridge deck.
In step 311, switching OFF of the cartridge-based device 101 may be performed. The ON/OFF switch is present at the rear of the device.
Referring to Figure 4, multiple different views of the Syringe Module 102 is illustrated, in accordance with an embodiment of the present disclosure. Figure 4a illustrates the top view of the Syringe Module 102. Figure 4b illustrates the perspective view of the Syringe Module 102. Figure 4c illustrates the side view of the Syringe Module 102. Figure 4d illustrates the front view of the Syringe Module 102.
Referring to Figure 5, multiple different views of the Detection Module 107 is illustrated, in accordance with an embodiment of the present disclosure. Figure 5a illustrates the top view of the Detection Module 107. Figure 5b illustrates the perspective view of the Detection Module 107. Figure 5c illustrates the side view of the Detection Module 107. Figure 5d illustrates the front view of the Detection Module 107.
Referring to Figure 6, multiple different views of the Thermo-Shaker Module 105 is illustrated, in accordance with an embodiment of the present disclosure. Figure 6a illustrates the top view of the Thermo-Shaker Module 105. Figure 6b illustrates the perspective view of the Thermo-Shaker Module 105. Figure 6c illustrates the side view of the Thermo-Shaker Module 105. Figure 6d illustrates the front view of the Thermo-Shaker Module 105
The method and system of cartridge-based device (101) for DNA/RNA extraction and PCR Amplification of a single sample, of the present subject matter offer following advantages, but are not limited to, following benefits/advantages:
• The ability to process one sample at a time will assist in rapid diagnosis and treatment of critically ill patients.
• By using a rotating mechanism rather than a to-and-fro mechanism, the machine has been made more compact, which also reduces the size and weight of the instrument.
• The chances of contamination are reduced since the syringe will pick up and drop the syringe in the same well from which it was picked.
• Automated DNA/RNA extraction and purification eliminate human error.
• The need to use large equipment that can handle 40 or more samples to process a single sample is eliminated.
• The precise syringe assembly design is unique and occupies minimum space.
• The PCR tube neck heating mechanism is unique. It assists in maintaining the temperature homogeneity in the tubes.
• Useful in clinical settings rather than laboratory. Thus, it eliminates huge capital investment and infrastructure of molecular labs to test a single sample.
• The Pre-setup time is significantly less for a single sample processing.
• Does not require high end technical expertise to run the system.
Various modifications to the embodiment will be readily apparent to those skilled in the art and the generic principles herein may be applied to other embodiments. However, one of ordinary skill in the art will readily recognize that the present disclosure is not intended to be limited to the embodiments illustrated but is to be accorded the widest scope consistent with the principles and features described herein.
The foregoing description shall be interpreted as illustrative and not in any limiting sense. A person of ordinary skill in the art would understand that certain modifications could come within the scope of this disclosure.
The embodiments, examples and alternatives of the preceding paragraphs or the description and drawings, including any of their various aspects or respective individual features, may be taken independently or in any combination. Features described in connection with one embodiment are applicable to all embodiments unless such features are incompatible.
,CLAIMS:We claim:
1. A portable, fully automated cartridge-based device 101 for processing a biological sample comprising of:
a. a cartridge tray 101, encasing a removable rotating cartridge deck, wherein the removable rotating cartridge deck may comprise a reaction tube and chambers.
b. a syringe module 102, wherein the syringe module with the help of a tip holder pierces an extraction well sealed, using a piercing needle or tip;
c. a syringe up-down mechanism 103, piercing the extraction well cover and aspiring/dispensing the reagents and chemicals in an assigned well;
d. a tip discard mechanism 104, wherein the said mechanism ensures the discarding of the used tip in an original well from which it was picked;
e. a thermo-shaker module 105, to heat the wells while shaking them to achieve homogenization;
f. a heating lid mechanism 106, to regulate the temperature of the reaction tube;
g. a detection module 107, for analysis and viewing of final PCR results;
h. an electronics 108, to receive input from a user and provide instructions to various modules of the cartridge-based device;
i. a cooling fan 109, to cool down the reaction tube;
j. a base plate 110, to hold modules of the cartridge-based device 101;
k. a thermocycler, placed under the cartridge deck in the tray, wherein the basal parts of the reaction tubes may be exposed to the thermal cycler;
l. a magnet mechanism 111 coordinating with the thermo-shaker module 105 for extraction of nucleic acids from biological samples; and
m. a one or more motors 112 to power the multiple modules of the cartridge-based device 101.
wherein the portable, fully automated cartridge-based device 101 automates ‘Sample-to-Result’ operations of nucleic acid extraction and PCR amplification of a single sample to detect, quantify, and identify various parameters.

2. The cartridge-based device (101) for processing biological samples as claimed in claim 1, wherein the removal and insertion of the rotating cartridge deck is fully automated and may be access-controlled via a digital screen associated with the cartridge Tray (101).

3. The cartridge-based device (101) for processing biological samples as claimed in claim 1, wherein the cartridge comprises a two-latch mechanism with interlocking latches that may secure the cartridge in place.

4. The cartridge-based device (101) for processing biological samples as claimed in claim 1, wherein the rotating cartridge deck may comprise:
a) a chamber 1, wherein the chamber 1 may have 10 wells having the reagents/chemicals required for nucleic acid extraction procedure;
b) a chamber 2, wherein the chamber 2 may have 6 wells having the master mix solutions required for the PCR reactions;
c) a chamber 3, wherein the chamber 3 may have 10 Tip holding wells;
d) a chamber 4, wherein the chamber 4 may have a single piercing plastic needle well; and
e) a chamber 5, wherein the chamber 5 may have 6 wells housing PCR tubes which will further undergo denaturation, annealing and extension steps of PCR.

5. The portable, fully automated cartridge-based device (101) for processing biological samples as claimed in claim 1, wherein electronics 108 may comprise processing chips, control units, and display screens.

6. A process for processing biological samples as claimed in claim 1 to 5 using portable, fully automated cartridge-based device (101), comprising the steps of:
a. selecting 201 a protocol according to a sample and cartridge either automatically or manually;
b. adding manually 202 samples in the reaction tube with an adequate buffer;
c. placing 203 the reaction tube in the thermoshaker module 105;
d. piercing extraction wells 204 using a piercing tip with the help of tip holder;
e. returning 205 the piercing tip to original position after piercing extraction wells;
f. piercing the PCR mix well 206 using another piercing tip with the help of tip holder;
g. returning 207 the piercing tip to original position after piercing PCR wells;
h. discarding 208 the used needles into their original position with the help of the tip discard mechanism;
i. mixing and heating 209 all the reagents and samples in the reaction tube using thermoshaker module 105 and extracting nucleic acid using magnetic bead-based technology 111;
j. eluting buffer 210 and pure nucleic acid in a defined well based on selected protocol;
k. piercing 301 the sealed PCR mix wells using a piercing needle or tip;
l. aspirating/ dispensing 302 extracted nucleic acid into the master mix using new tips and dispensing the mixture from the six wells to corresponding PCR tubes;
m. closing 303 PCR tubes caps by tip holder;
n. applying 304 heating lids to PCR tubes tops;
o. positioning 305 optical Fiber holder above heating leads;
p. placing the reaction tubes in the thermal cycler 306, wherein a Peltier belt mechanism assists in heating and cooling required for a PCR process;
q. transmitting and receiving LED signals 307 between the rotating detection module 107 and reaction tubes via optical fibers from a top and receiving the signals via the branched optical fibers to the detection module;
r. transforming received optical signal into electrical signal 308 and displaying fluorescence graph on a digital screen;
s. performing flexible customization 309 through a user interface on the screen;
t. disposing off the used cartridge followed by UV illumination to sterilize the cartridge deck; and
u. switching of the cartridge deck.

7. The process for processing biological samples as claimed in claim 6, wherein the thermal cycler is placed under the cartridge deck in the tray and basal parts of the PCR tubes may be exposed to the thermal cycler.

8. The process for processing biological samples as claimed in claim 6, wherein to counteract the Peltier's heat, a heat sink is positioned beneath the thermal cycler.